Methods and Compositions for Cannabis Characterization

ABSTRACT

Provided are methods for determining if a cannabis sample comprises hemp or marijuana, or  Cannabis sativa  and/or  Cannabis indica  as well as primers and kits for use in the methods.

FIELD

The present disclosure provides methods, compositions and kits for characterizing cannabis samples. The present disclosure also provides method, compositions and kits for distinguishing Cannabis sativa from Cannabis indica, and marijuana from hemp as well as measuring contribution of Cannabis sativa and Cannabis indica in marijuana.

BACKGROUND

Cannabis is one of humanity's oldest crops, with records of use dating to 6000 years before present. It is used as a source of high-quality bast fibre, nutritious and oil-rich seeds and for the production of cannabinoid compounds including delta-9 tetrahydrocannabinol (THC) and cannabidiol (CBD). The evolutionary history and taxonomy of Cannabis remains poorly understood. Hillig (2005) proposed that the genus Cannabis consists of three species (C. sativa, C. indica , and C. ruderalis) [1], whereas an alternative viewpoint is that Cannabis is monotypic and that observable subpopulations represent subspecies of C. sativa: C. sativa subspecies sativa, C. sativa subspecies indica and C. sativa subspecies ruderalis [2]. The putative ruderalis type may represent feral populations of the other types or those adapted to northern regions. The classification of Cannabis populations is confounded by many cultural factors, and tracing the history of a plant that has seen wide geographic dispersal and artificial selection by humans over thousands of years has proven difficult. Many hemp types have varietal names while marijuana types lack an organized horticultural registration system and are referred to as strains. The draft genome and transcriptome of C. sativa were published in 2011 [3]. As both public opinion and legislation in many countries shifts towards recognizing Cannabis as a plant of medical and agricultural value [4], the genetic characterization of marijuana and hemp becomes increasingly important for both clinical research and crop improvement efforts.

Differences between Cannabis sativa and Cannabis indica have been reported.

Although the taxonomy of the genus Cannabis remains unclear, many breeders, growers and users (patients) consuming cannabis for its psychoactive and/or medicinal properties differentiate Sativa-type from Indica-type plants.

Hillig & Mahlberg (2004) [20] have reported that mean THC levels and the frequency of the THCA synthase gene (B_(T) allele) were significantly higher in C. indica than C. sativa. Plants with relatively high levels of tetrahydrocannabivarin (THCV) and/or cannabidivarin (CBDV) were common only in C. indica.

Hazekamp & Fischedick (2011) [10] summarized differences between typical Sativa and Indica effects upon smoking. As a result of limited understanding and support from the medical community, they indicate that medicinal users of cannabis generally adopt the terminology derived from recreational users to describe the therapeutic effects they experience.

They report that the psychoactive effects (the “high”) from Sativa-type plants are often characterized as uplifting and energetic. The effects are mostly cerebral (head-high), and are also described as spacey or hallucinogenic. Sativa is considered as providing pain relief for certain symptoms. In contrast, the high from Indica-type plants is most often described as a pleasant body buzz (body-high or body stone). Indices are primarily enjoyed for relaxation, stress relief, and for an overall sense of calm and serenity and are supposedly effective for overall body pain relief and in the treatment of insomnia.

They reported that the most common way currently used to classify cannabis cultivars is through plant morphology (phenotype) with Indica-type plants smaller in height with broader leaves, while Sativa-type plants taller with long, narrow leaves. Indica-type plants typically mature faster than Sativa-type plants under similar conditions, and the types tend to have a different smell, perhaps reflecting a different profile of terpenoids.

There remains a need for more accurate classification of cannabis for medicinal and other commercial purposes.

SUMMARY

Using 14,031 single-nucleotide polymorphisms (SNPs) genotyped in 81 marijuana and 43 hemp samples, marijuana and hemp are found to be significantly differentiated at a genome-wide level, demonstrating that the distinction between these populations is not limited to genes underlying THC production.

In addition, using additional SNPs including a second set of 9123 SNPs genotyped in 37 reported Cannabis indica and 63 reported Cannabis sativa samples, ancestry determinations could be made which can be used for example for selecting breeding partners.

Other features and advantages of the present disclosure will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples while indicating preferred embodiments of the disclosure are given by way of illustration only, since various changes and modifications within the spirit and scope of the disclosure will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

An embodiment of the present disclosure will now be described in relation to the drawings in which:

FIG. 1. Genetic structure of marijuana and hemp. (a) Principal Components Analysis (PCA) plot of 42 hemp and 80 marijuana samples using 14,031 SNPs. Hemp samples are closed circles and marijuana samples are open circles. The proportion of the variance explained by each Principal Component (PC) is shown in parentheses along each axis. The two samples labeled with their IDs are discussed in the text. (b) Boxplots showing significantly lower heterozygosity in marijuana than in hemp. (c) Population structure of hemp and marijuana estimated using the fastSTRUCTURE admixture model at K=2. Each sample is represented by a thin vertical line, which is partitioned into two colored segments that represent the sample's estimated membership in each of the two inferred clusters. Hemp and marijuana samples are labeled below the plot.

FIG. 2. Genetic structure of marijuana. (a) PCA plot of 81 marijuana samples using 9,776 SNPs. Samples are shaded according to their reported C. sativa ancestry. The proportion of the variance explained by each PC is shown in parentheses along each axis. (b) Population structure of marijuana calculated using the fastSTRUCTURE admixture model at K=2. Each sample is represented by a horizontal bar, which is partitioned into two segments that represent the sample's estimated membership in each of the two inferred clusters. Adjacent to each bar is the sample's name and reported % C. sativa ancestry. (c) The correlation between the principal axis of genetic structure (PC1) in marijuana and reported C. sativa ancestry.

FIG. 3. Distribution of FST between marijuana and hemp samples across 14,031 SNPs. (a) FST distribution for all SNPs genotyped. (b) Distribution of SNPs with FST greater than 0.5. Average FST is weighted by allele frequency and was calculated according to equation 10 in Weir and Cockerham (1984) [19].

FIG. 4. Mean pairwise Identity by State (IBS) between each marijuana sample and all hemp samples versus reported C. sativa ancestry.

FIG. 5. Example PCA of 81 marijuana strains using 9776 SNPs.

FIG. 6. Example distribution of per-SNP F_(ST) values between 9 presumed C. indica and 9 presumed C. sativa strains.

FIG. 7. Example evaluation of panels of ancestry informative markers (AIMS). Accuracy is defined here as the correlation between the positions of non-ancestral samples along PC1 calculated using 9766 SNPs and the positions calculated using a given subset of AIMs.

FIG. 8. Example PCA of 100 marijuana strains using 9123 SNPs.

DETAILED DESCRIPTION OF THE DISCLOSURE

The term “cannabis reference” as used herein means a cannabis strain, species (e.g. sativa or indica) (also referred to as subspecies (e.g. sativa or indica)) or type (marijuana or hemp) with at least some known genotype profile information which is used as a reference comparison to a test sample, optionally wherein the genotype and/or allele frequency of at least 10 SNPs in Table 4, 5 and/or 8 are known, optionally all of the SNPs in any one of Tables 4, 5 and/or 8. The cannabis reference can be a Cannabis sativa reference, Cannabis indica reference, marijuana reference or hemp reference or a reference profile of any of the foregoing.

The term “Cannabis sativa reference” and “Cannabis indica reference” as used herein mean respectively, a selected Cannabis sativa strain or Cannabis indica strain which is used as a reference for comparison and/or genotype information of such a strain or genotype information associated with the particular Cannabis sativa or Cannabis indica reference strain e.g. a reference profile for a particular strain or a reference profile associated with the species. The reference profile comprises at least 10 known SNPs (e.g. genotype and optionally frequency) in Table 4 and/or Table 8, optionally all of the SNPs in Table 4 and/or 8 found in the particular Cannabis sativa or Cannabis indica strain respectively or a composite of strains of the particular species. The Cannabis sativa reference or Cannabis indica reference can include in addition to the predominant allele in the species or a particular strain of the species the frequency of the SNP allele in the population.

The term “cannabis reference profile” as used herein means genotype information of one (e.g. a particular strain) or plurality of cannabis strains and/or species, including Cannabis sativa and/or Cannabis indica strains or marijuana and/or hemp strains, and includes the genotype of at least 10 SNPs in Table 4, 5 and/or 8, optionally all of the SNPs in Table 4, 5 and/or 8. A Cannabis sativa reference profile as used herein means genotype information of a plurality of cannabis strains and includes genotype sequence (and optionally including frequency information) associated with Cannabis sativa strains and a Cannabis indica reference profile as used herein means genotype information of a plurality of cannabis strains and includes genotype sequence (and optionally including frequency information) associated with Cannabis indica strains.

The term “marijuana” as used herein denotes cannabis plants and plant parts that are cultivated and consumed as a drug or medicine. Marijuana often contains high amounts of psychoactive cannabinoids such as tetrahydrocannabinolic acid (THCA) and delta-9 tetrahydrocannabinol (THC) but it may also contain cannabidiolic acid (CBDA) and cannabidiol (CBD). For example, marijuana can be defined as cannabis plants and plant parts wherein the leaves and flowering heads of contain more than 0.3% w/w, 0.4% w/w or 0.5% w/w of delta-9-tetrahydrocannabinol (THC) (dry weight). The term “hemp” as used herein denotes cannabis plants that are cultivated and used for the production of fibre or seeds rather than as drug or medicine. Often hemp plants often contain high amounts of CBDA and CBD, and low amounts of THCA and THC. For example, hemp can be defined as cannabis plants and plant parts wherein the leaves and flowering heads of which do not contain more than 0.3% w/w, 0.4% w/w or 0.5% w/w of delta-9-tetrahydrocannabinol (THC) (dry weight).

The term “polynucleotide”, “nucleic acid”, “nucleic acid molecule” and/or “oligonucleotide” as used herein refers to a sequence of nucleotide or nucleoside monomers consisting of naturally occurring and/or modified bases, sugars, and intersugar (backbone) linkages, and is intended to include DNA and RNA which can be either double stranded or single stranded, representing the sense or antisense strand.

As used herein, the term “isolated nucleic acid molecule” refers to a nucleic acid substantially free of cellular material or culture medium when produced by recombinant DNA techniques, or chemical precursors, or other chemicals when chemically synthesized. The term “nucleic acid” is intended to include DNA and RNA and can be either double stranded or single stranded.

The term “primer” as used herein refers to a nucleic acid molecule, whether occurring naturally as in a purified restriction digest or produced synthetically, which is capable of acting as a point of synthesis of when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid strand is induced (e.g. in the presence of nucleotides and an inducing agent such as DNA polymerase and at a suitable temperature and pH). The primer must be sufficiently long to prime the synthesis of the desired extension product in the presence of the inducing agent. The exact length of the primer will depend upon factors, including temperature, sequences of the primer and the methods used. A primer typically contains 15-25 or more nucleotides, although it can contain less, for example 10 nucleotides. The factors involved in determining the appropriate length of primer are readily known to one of ordinary skill in the art.

As used herein, the term “upstream primer” as used herein refers to a primer that can hybridize to a DNA sequence and act as a point of synthesis upstream, or at a 5′, of a target polynucleotide sequence e.g. SNP, to produce a polynucleotide complementary to the target polynucleotide anti-sense strand. The term “downstream primer” as used herein refers to a primer that can hybridize to a polynucleotide sequence and act as a point of synthesis downstream, or at a 3′ end, of a target polynucleotide sequence, to produce a polynucleotide complementary to the target polynucleotide sense strand.

The term “probe” as used herein refers to a polynucleotide (interchangeably used with nucleic acid) that comprises a sequence of nucleotides that will hybridize specifically to a target nucleic acid sequence. For example the probe comprises at least 18 or more bases or nucleotides that are complementary and hybridize to contiguous bases and/or nucleotides in the target nucleic acid sequence. The length of probe depends on the hybridization conditions and the sequences of the probe and nucleic acid target sequence and can for example be 10-20, 21-70, 71-100 or more bases or nucleotides in length. The probes can optionally be fixed to a solid support such as an array chip or a microarray chip. For example, the PCR product produced with the primers could be used as a probe. The PCR product can be for example be subcloned into a vector and optionally digested and used as a probe.

The term “reverse complement” or “reverse complementary”, when referring to a polynucleotide, as used herein refers to a polynucleotide comprising a sequence that is complementary to a DNA in terms of base-pairing and which is reversed so oriented from the 5′ to 3′ direction.

As used herein, the term “kit” refers to a collection of products that are used to perform a reaction, procedure, or synthesis, such as, for example, a genotyping assay etc., which are typically shipped together, usually within a common packaging, to an end user.

The term “target allele” as used herein means an allele for a SNP listed in Table 4, 5 or 8.

The term “major allele” as used herein is the allele most commonly present in a population. The major allele listed in Tables 4, 5 and 8 is the allele most commonly present in Cannabis sativa and Cannabis indica strains (Tables 4 and 8) and marijuana and hemp strains (Table 5) respectively.

The term “minor allele” as used herein is the allele least commonly present in a population (e.g. C. sativa and C. indica or marijuana and hemp). The minor allele listed in Tables 4, 5 and 8 is present in the frequency indicated therein.

A single-stranded nucleic acid molecule is “complementary” to another single-stranded nucleic acid molecule when it can base-pair (hybridize) with all or a portion of the other nucleic acid molecule to form a double helix (double-stranded nucleic acid molecule), based on the ability of guanine (G) to base pair with cytosine (C) and adenine (A) to base pair with thymine (T) or uridine (U).

The term “hybridize” as used herein refers to the sequence specific non-covalent binding interaction with a complementary nucleic acid.

The term “selectively hybridize” as used herein refers to hybridization under moderately stringent or highly stringent physiological conditions, which can distinguish related nucleotide sequences from unrelated nucleotide sequences. In nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency are known to vary, depending on the nature of the nucleic acids being hybridized, including, for example, the length, degree of complementarity, nucleotide sequence composition (e.g., relative GC:AT content), and nucleic acid type, i.e., whether the oligonucleotide or the target nucleic acid sequence is DNA or RNA. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter, bead, chip, or other solid matrix. Appropriate stringency conditions which promote hybridization are known to those skilled in the art, or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1 6.3.6 and/or Current Protocols in Nucleic Acid Chemistry available at http://onlinelibrary.wiley.com/browse/publications?type=lab protocols.

As used in this application, the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “include” and “includes”) or “containing” (and any form of containing, such as “contain” and “contains”), are inclusive or open-ended and do not exclude additional, unrecited elements or process steps.

As used in this application and claim(s), the word “consisting” and its derivatives, are intended to be close ended terms that specify the presence of stated features, elements, components, groups, integers, and/or steps, and also exclude the presence of other unstated features, elements, components, groups, integers and/or steps.

The term “consisting essentially of”, as used herein, is intended to specify the presence of the stated features, elements, components, groups, integers, and/or steps as well as those that do not materially affect the basic and novel characteristic(s) of these features, elements, components, groups, integers, and/or steps.

The terms “about”, “substantially” and “approximately” as used herein mean a reasonable amount of deviation of the modified term such that the end result is not significantly changed. These terms of degree should be construed as including a deviation of at least ±5% of the modified term if this deviation would not negate the meaning of the word it modifies.

As used in this application, the singular forms “a”, “an” and “the” include plural references unless the content clearly dictates otherwise. For example, an embodiment including “a compound” should be understood to present certain aspects with one compound or two or more additional compounds.

Further, the definitions and embodiments described in particular sections are intended to be applicable to other embodiments herein described for which they are suitable as would be understood by a person skilled in the art. For example, in the following passages, different aspects of the invention are defined in more detail. Each aspect so defined may be combined with any other aspect or aspects unless clearly indicated to the contrary. In particular, any feature indicated as being preferred or advantageous may be combined with any other feature or features indicated as being preferred or advantageous.

III. Methods and Products

The present disclosure identifies for example a plurality of single nucleotide polymorphisms (SNPs) ancestry informative markers (AIMs) that can be used to characterize cannabis samples. Cannabis samples can be characterized for example according to their ancestral relatedness and/or whether the sample is likely marijuana or hemp. Accordingly, the present disclosure provides methods, nucleic acids, primers and kits useful for detecting whether a sample is Cannabis sativa dominant or Cannabis indica dominant, for assessing the relatedness of a test sample to Cannabis sativa and/or Cannabis indica reference samples as well as methods, nucleic acids, primers and kits for distinguishing marijuana from hemp. Also provided are a computer implemented method, a computer program embodied on a computer readable medium, a system, apparatus and/or processor for carrying out a method or part thereof described herein.

Embodiments of the methods and systems described herein may be implemented in hardware or software, or a combination of both. These embodiments may be implemented in computer programs executing on programmable computers, each computer including at least one processor, a data storage system (including volatile memory or non-volatile memory or other data storage elements or a combination thereof), and at least one communication interface. For example, and without limitation, the various programmable computers may be a server, network appliance, set-top box, embedded device, computer expansion module, personal computer, laptop, mobile telephone, smartphone or any other computing device capable of being configured to carry out the methods described herein.

The data storage system may comprise a database, such as on a data storage element, in order to provide a database of Cannabis reference strains, and/or reference profiles. Furthermore, computer instructions may be stored for configuring the processor to execute any of the steps and algorithms described herein as a computer program.

Each program may be implemented in a high level procedural or object oriented programming or scripting language, or both, to communicate with a computer system. However, alternatively the programs may be implemented in assembly or machine language, if desired. The language may be a compiled or interpreted language. Each such computer program may be stored on a non-transitory computer readable storage medium (e.g. read-only memory, magnetic disk, optical disc). The storage medium so configured causes a computer to operate in a specific and predefined manner to perform the functions described herein.

An aspect of the present method for detecting the presence or absence of each of a set of target alleles in a cannabis sample, the method comprising:

I) obtaining a test sample comprising genomic DNA, and

II) either

-   -   i) genotyping the test sample for a set of single nucleotide         polymorphisms (SNPs), the set comprising at least 10, 20, 30,         40, 48, 50, 60, 70, 80, 90, 96, 100 or any number between and         including 10-200 of the SNPs in Table 4 and/or 8, wherein each         SNP comprises a major allele and a minor allele as provided in         Table 4 and 8; and     -   ii) detecting for each SNP of the set the presence or absence of         the major allele and/or the minor allele in the test sample; or     -   a) genotyping the test sample for a set of SNPs, the set at         least 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96 or 100 of the         comprising the SNPS in Table 5, wherein each SNP comprises a         major allele and a minor allele as provided in Table 5; and     -   b) detecting for each SNP of the set the presence or absence of         the major allele and/or the minor allele in the test sample.

In an embodiment, the SNPS in Table 4 and/or 8 can be used to determine the ancestral contribution of Cannabis sativa and/or Cannabis indica in a marijuana strain.

The step of obtaining a test sample comprising genomic DNA can be accomplished, for example by taking the cannabis sample or an aliquot thereof for example if the cannabis sample is isolated genomic DNA, or can comprise preparing an isolated genomic DNA from the cannabis sample or a portion thereof.

The cannabis sample or the test sample (e.g. comprising at least a portion of the cannabis sample) is any cannabis sample comprising genomic DNA. The sample can be isolated genomic DNA or a portion of a plant and/or seed comprising genomic DNA and optionally from which genomic DNA can be isolated. For example, the test sample can be a plant sample, a seed sample, a leaf sample, a flower sample, a trichome sample, a pollen sample a sample of dried plant material including leaf, flower, pollen and/or trichomes, or a sample produced through in vitro tissue or cell culture. Genomic DNA can be isolated using a number of techniques such as NaOH extraction, phenol/chloroform extraction, DNA extraction systems such as Qiagen Direct PCR DNA Extraction System (Cedarlane, Burlington ON). In some embodiments, genomic DNA is not purified prior to genotyping. For example, with the Phire Plant Direct PCR Kit the DNA target can be used to detect SNP alleles without prior DNA extraction (Life Technologies, Burlington ON).

In an embodiment, the set of target alleles which are detected are a plurality of SNPs in Tables 4, 5 and/or 8. Tables 4 and 8 each list 100 SNPs, including a major allele and a minor allele and the minor allele frequency in Cannabis sativa strains and Cannabis indica strains. Table 5 lists 100 SNPs including a major allele and a minor allele and the minor allele frequency in marijuana and hemp. Also described in these Tables is the SNP position in the canSat3 C. sativa reference genome assembly which is described in van Bakel et al [3], identified as the SNP name. The genome build assembly is identified by the number 3 for SNPs defined by SEQ ID NOs:1-400 (CanSat3) and the number 5 for SNPs defined by SEQ ID Nos: 401-600 (CanSat5). Tables 6, 7 and 9 also identify the upstream+SNP and downstream sequences associated with each SNP. A person skilled in the art would understand that genomic DNA is double stranded and that the complementary nucleotide on the reverse strand can also be detected based on the complementary base pairing rules.

Genotyping the cannabis sample at the loci listed for example in Tables 4, 5 and 8 can be accomplished by various methods and platforms.

In an embodiment, the step of genotyping comprises sequencing genomic DNA for example using a genotyping by sequencing (GBS) method. GBS is typically a multiplexed approach involving tagging randomly sheared DNA from different samples with DNA barcodes and pooling the samples in a sequencing reaction. Target enrichment and/or reduction of genome complexity for example using restriction enzymes.

In another embodiment, the step of genotyping comprises sequencing pooled amplicons, including captured amplicons. In an embodiment, the amplicons are produced using primers flanking the SNPs, for example within 100 nucleotides upstream and/or within 100 nucleotides downstream of the SNP location and amplifying targeted region. The resulting amplification products are then sequenced. Forward primers and reverse primers that amplify for example 25 or more nucleotides surrounding and including the SNP can be used in such genotyping methods.

A variety of sequencing methods can be employed including electrophoresis-based sequencing technology (e.g. chain termination methods, dye-terminator sequencing), by hybridization, mass spectrometry based sequencing, sequence-specific detection of single-stranded DNA using engineered nanopores and sequencing by ligation. For example, amplified fragments can be purified and sequenced directly or after gel electrophoresis and extraction from the gel.

Other PCR based genotyping methods can also be used optionally comprising DNA amplification using forward and reverse primers and/or primer extension.

For example the iPLEX Gold Assay by Sequenom® provides a SNP genotyping assay where PCR primers are designed in a region of approximately 100 base pairs around the SNP of interest and an extension primer is designed adjacent to the SNP. The method involves PCR amplification followed by the addition of Shrimp alkaline phosphatase (SAP) to inactivate remaining nucleotides in the reaction. The primer extension mixture is then added and the mixture is deposited on a chip for data analysis by a TM MALDI-TOF mass spectrometer (Protocol Guide 2008).

In another embodiment, the genotyping method comprises using an allele specific primer. An example is the KASP™ genotyping system is a fluorescent genotyping technology which uses two different allele specific competing forward primers with unique tail sequences and one reverse primer. Each unique tail binds a unique fluorescent labelled oligo generating a signal upon PCR amplification of the unique tail.

In an embodiment, allele specific probes are utilized. For example, an allele specific probe includes the complementary residue for the target allele of interest and under specified conditions preferentially binds the target allele. The probe can comprise a DNA or RNA polynucleotide and the genotyping step can comprise contacting the test sample with a plurality of probes each of the probes specific for a SNP allele of the set of SNPs under conditions suitable for detecting for example the minor SNP alleles.

In an embodiment, the genotyping method comprises using an array. The array can be a fixed or flexible array comprising for example allele specific probes. The array can be a bead array for example as is the Infinium HD Assay by Illumina. In an embodiment, the array comprises primers and/or probes using sequences or parts thereof described in SEQ ID Nos: 1-600. The array format can comprise primers or probes for genotyping for example at least 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96 or 100 or more SNPs, for example any number between and including 1 and 300, optionally 10 and 300 or 10 and 200 or 10 and 100. In an embodiment, the array format comprises one or more primers or probes for each SNP. In an embodiment, the array comprises 96 reactions.

Upstream sequence, the SNP as well as downstream sequence for the SNPs in Tables 4, 5 and 8 are provided in Tables 6, 7 and 9.

As demonstrated in FIG. 7, a level of accuracy can be achieved using the 10 SNPs with the highest Fst values. Accordingly in one embodiment, the set of SNPs comprises the first listed 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96 or 100 SNPs or any number or combination of SNPs between and including 10 and 300, optionally 10 and 100 in Table 4, 5 or 8, optionally any combination of SNPs in Tables 4 and/or 8. In an embodiment, the set of SNPs comprises a plurality or all of the SNPs in Table 4 and/or 8 with a Fst of greater than 0.712 or 06277. In another embodiment, the set of SNPs comprises a plurality or all of the SNPs in Table 5 with a Fst of greater than 0.679. In an embodiment, the set of SNPs includes at least 2 wherein the allele frequency is 0.

In an embodiment, any number of SNPS listed in Tables 4 and/or 8, or Table 5 is genotyped.

In an embodiment, a plurality of SNPs listed in Tables 4 and/or 8 and 5 are detected. In such methods, both ancestry contribution and marijuana versus hemp assessments can be conducted in one assay.

In an embodiment, the step of detecting the SNP comprises receiving, reviewing and/or extracting from a file, document, reaction, array or database, the genotype for each of the SNPs of the set.

In certain embodiments, the method further comprises displaying and/or providing a document displaying one or more features of the major and/or minor alleles. For example, the one or more features can comprise the position of the SNP, the nucleotide identity of the SNP or the nucleotide identity if a minor allele is detected, the number of reads or reaction, the number of minor alleles, confidence intervals etc. The document can be an electronic document that is provided to a third party. In an embodiment, the one or more features displayed is selected from the allele nucleotide identity and the number of minor alleles in common with Cannabis sativa, Cannabis indica, marijuana or hemp.

As demonstrated herein, the SNP allele information can be used to characterize the cannabis sample. Accordingly, in an embodiment, the method further comprises determining ancestry contribution of the test sample.

The ancestry contribution is optionally an ancestry contribution estimate or identification of ancestry dominance. For example, the ancestry dominance of the test sample can be Cannabis sativa dominant or Cannabis indica dominant according to the set of target alleles detected in step II) ii). If the target alleles in combination when compared to a database of cannabis reference strains and/or the reference profiles provided in Table 4 and 8 are most similar to alleles more commonly found in Cannabis sativa, for example if greater than 50% of the cannabis sample's SNPs are alleles more commonly present in Cannabis sativa, the cannabis sample is identified as Cannabis sativa dominant. Conversely, if the target alleles in combination are most similar to alleles more commonly found in Cannabis indica, for example if greater than 50% of the cannabis sample's SNPs are alleles more commonly present in Cannabis indica, the cannabis sample is identified as Cannabis indica dominant.

An ancestry contribution estimate is calculated in one embodiment, according to a method described in the Examples. Other calculations for determining admixture can also be applied as further described herein.

Other nucleotides may be detected at the SNP positions described or a particular reaction may fail. In an embodiment, if an allele other than an allele reported in Tables 4, 5 and 8 is detected or if the nucleotide at the position is unknown, the allele is not considered in the methods described.

An ancestry contribution estimate can identify a population structure that is associated or is most likely given the nucleotide occurrences of the SNPs in the cannabis sample.

In an embodiment, the method further comprises identifying the test sample as marijuana or hemp, according to the set of target alleles detected in step II) b). A cannabis sample is identified as hemp for example if the target alleles in combination when compared to a database of cannabis reference strains and/or the reference profiles provided in Table 5 are most similar to alleles more commonly found in hemp, the cannabis sample is identified as hemp. Conversely, if the target alleles in combination are most similar to alleles more commonly found in marijuana, the cannabis sample is identified as marijuana.

An aspect accordingly includes a method of determining ancestry contribution of a cannabis sample, optionally to determine if a sample comprises nabis sativa and/or Cannabis indica, the method comprising:

I) obtaining a test sample comprising genomic DNA,

II) i) genotyping the test sample for a set of single nucleotide polymorphisms (SNPs), the set comprising at least 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96 or 100 or more of the SNPs in Table 4 and/or 8, wherein each SNP comprises a major allele and a minor allele as provided in Table 4 and 8; and

-   -   ii) detecting for each SNP of the set the presence or absence of         the major allele and/or the minor allele in the test sample; and

III) determining ancestry contribution of the test sample according to the set of target alleles detected in step II) ii and providing an estimate of the ancestry contribution or the identifying the test sample as Cannabis sativa dominant or Cannabis indica dominant.

As mentioned above, dominance is assigned as Cannabis sativa dominant or Cannabis indica dominant according to the similarity of the detected alleles. If the set of detected alleles, when compared to a database of cannabis reference strains and/or the reference profiles provided in Table 4 and/or 8 are most similar to alleles more commonly found in Cannabis sativa as indicated in Table 4 and 8, the cannabis sample is assigned as Cannabis sativa dominant. Similarly, if the set of detected alleles are most similar to alleles more commonly found in Cannabis indica as indicated in Table 4 and 8, the cannabis sample is assigned as Cannabis indica dominant.

In an embodiment, the method further comprises selecting a breeding partner.

The ancestry estimates can be used for example to identify Sativa- or Indica-type breeding individuals when classification is unknown or unsure. As an example, the SNPs described herein can be used to breed an offspring with a desired or defined contribution, for example about equal contribution, of Cannabis indica and Cannabis sativa genetic material. The SNPs in Table 4, 5 and 8 can be used to select for marijuana and hemp, or Indica- and Sativa-type strains with the desired ancestry contribution for use as parents.

For example, these markers can be used in marker-assisted selection (MAS) to breed cannabis plants that contain defined levels of Indica-type or Sativa-type ancestry.

As another example SNPs as described herein can be used in ancestry selection breeding and used to speed the recovery of the cultivated genetic background (as described in [22]). For example in a cross between a cultivated line and a wild line, the F1 offspring generated from such a cross necessarily derive 50% of its ancestry from each parent. On backcrossing to the cultivated line, each offspring will differ in the proportion of its ancestry from the wild and cultivated sources. Genetic markers distributed across the genome can be used to provide an estimate of the ancestry proportions, and the breeder can then select the offspring with the highest proportion of cultivated ancestry. Such methods can for example be performed with marker assisted selection (which uses trait associated markers), to select a small number of offspring in each generation that carry both the desired trait from the wild and the most cultivate ancestry.

In an embodiment, the method is for assessing if the cannabis sample is marijuana. For example, the marijuana can be for medical use.

Also provided is a set of SNPs that can be used to determine if a sample comprises hemp or marijuana. Accordingly another aspect includes a method for determining if a sample likely comprises hemp and/or marijuana, the method comprising:

I) obtaining a test sample comprising genomic DNA,

II) a) genotyping the test sample for a set of single nucleotide polymorphisms (SNPs), the set comprising at least 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96 or 100 of the SNPs in Table 5, wherein each SNP comprises a major allele and a minor allele as provided in Table 5; and

-   -   b) detecting for each SNP of the set the presence or absence of         the major allele and/or the minor allele in the test sample; and

III) identifying whether the sample likely comprises hemp or marijuana according to the set of target alleles detected in step II) b).

In an embodiment, the method is for differentiating medicinal/drug/pharmaceutical and non-medicinal/non-drug/non-pharmaceutical cannabis.

The identifying step comprises for example comparing to a database of reference alleles and/or comparing to the reference profiles in Table 5. The comparing step is further described below.

A further aspect includes a method for measuring genetic relatedness of a cannabis sample to a Cannabis sativa reference and/or a Cannabis indica reference, the method comprising:

I) obtaining a test sample comprising genomic DNA,

II) i) genotyping the test sample for a set of single nucleotide polymorphisms (SNPs), the set comprising at least 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96, 100 or any number between 10 and 200 of the SNPs in Table 4 and/or 8, wherein each SNP comprises a major allele and a minor allele as provided in Table 4 and 8; and

-   -   ii) detecting for each SNP of the set the presence or absence of         the major allele and/or the minor allele in the test sample;

III) comparing the test sample SNP to the Cannabis sativa reference and/or Cannabis indica reference according to the set of target alleles detected in step II) and

IV) displaying and/or providing a document displaying the calculated genetic relatedness of the test sample.

In an embodiment, the detecting, identifying and/or comparing step comprises calculating the genetic relatedness of the test sample to the cannabis reference, optionally a Cannabis sativa reference and/or Cannabis indica reference according to the set of target alleles detected in step II). The comparing step in an embodiment is carried out using a computer, for example a computer comprising a database for storing reference profiles for one or more strains or for the particular Cannabis sativa reference and/or Cannabis indica reference.

In an embodiment, the Cannabis sativa reference and/or the Cannabis indica reference is a reference profile or plurality of reference profiles stored in a database. The reference profile can for example include the SNP allele identities (e.g. minor allele) in Table 4 and/or 8 and its frequency for the species (e.g. a master reference profile) or the SNP allele identities of a particular strain.

In some embodiments, the reference is a reference sample and the method can comprise genotyping one or more reference samples and the test sample and comparing the detected alleles to identify the number of matches.

A further aspect includes a method for measuring a genetic relatedness of a Cannabis sativa sample to a reference marijuana or reference hemp sample, the method comprising:

I) obtaining a test sample comprising genomic DNA,

II) a) genotyping the test sample for a set of single nucleotide polymorphisms (SNPs), the set comprising at least 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96 or 100 of the SNPs in Table 5, wherein each SNP comprises a major allele and a minor allele as provided in Table 5; and

-   -   b) detecting for each SNP of the set the presence or absence of         the major allele and/or the minor allele in the test sample;

III) calculating the genetic relatedness of the test sample to the marijuana reference and/or the hemp reference according to the set of target alleles detected in step II) b; and

IV) displaying and/or providing a document displaying the calculated genetic relatedness of the test sample.

The method of determining ancestry contribution and/or the comparison for identifying the sample can involve use of a specifically programmed computer using for an example an algorithm to 1) compare the identity of the allele e.g whether the major and/or minor allele is detected, for each of the set of SNPs genotyped in the test sample to one or more cannabis references optionally compared to a database comprising a cannabis reference profile such as a master cannabis profile or a plurality of reference profiles, wherein each cannabis reference profile comprises genotype information for the set of SNPs detected; and 2) assign or calculate the ancestry contribution of the cannabis sample. Any algorithm for admixture analyses can be used. Computer implemented clustering and assignment protocols can also be used. The comparing step can also comprise comparing the relative frequency differences.

For example as demonstrated herein, the algorithm can direct a principle components analysis or a fastStructure analysis. For example, as demonstrated herein, principal component axes can be established using a plurality of cannabis reference strains and/or reference profiles. A cannabis sample genotype can be projected onto the two PCs. The ancestry contribution of Cannabis sativa for example can then be calculated using the formula:

% Cannabis sativa+b/(a+b)′,

wherein the a and b are the chord distances along the first principal component from the centroids of the Cannabis sativa strains and the Cannabis indica strains respectively.

In an embodiment, the algorithm is an algorithm described in the Examples.

Both the major allele and the minor allele can be detected in a test sample which can be used in determining the ancestry and/or assessing marijuana and/or hemp relatedness.

Also described herein are isolated nucleic acids, for example as primers or probes to detect the SNPs described herein. Accordingly another aspect includes an isolated nucleic acid comprising at least 9, 12, 15 or at least 18 contiguous nucleotides of any one of SEQ ID Nos 1-600 or the complement thereof.

In an embodiment, the isolated nucleic acid is a probe and comprises at least 12 or at least 18 nucleotides of contiguous sequence including the minor or major allele nucleotide; optionally including upstream sequence and/or downstream sequence contiguous with the minor or major allele.

In an embodiment, the nucleic acid is a primer comprising an isolated nucleic acid described herein.

In an embodiment, the primer is a forward PCR primer that hybridizes with a contiguous set of residues within 1-100 of any one of odd numbered SEQ ID Nos 1-600 or the, complement or reverse complement of residues 1-100 of any one of odd numbered SEQ ID Nos 1-600. In another embodiment, the primer is a reverse PCR primer (downstream primer) that hybridizes with residues 1 to 100 of any one of even numbered SEQ ID Nos 1-600 or the complement or the reverse complement with residues 1 to 100 of any one of even numbered SEQ ID Nos 1-600.

In another embodiment, the primer is an allele specific primer for a major allele and/or a minor allele in Table 4, 5 or 8 and binds to residue 101 of any one of odd numbered SEQ ID Nos 1-600. The odd numbered SEQ ID NOs comprise upstream sequence (for example 10 or more nucleotides) and the SNP allele at position 101 (e.g. 90-101). The even numbered SEQ ID NOs provide downstream sequence as indicated Tables 6, 7 and 9. For example SEQ ID NO:1 provides upstream sequence for SNP scaffold14566:24841 at nucleotides 1-100 and the SNP at nucleotide 101. SEQ ID NO:2 provides downstream sequence for this SNP.

In another embodiment, the primer is a primer extension primer and binds to residue 101 of any one of any one of odd numbered SEQ ID Nos 1-600.

Another aspect includes a plurality of primers for detecting a SNP allele in Table 4, 5 and/or 8, wherein the plurality comprises as least 2 different primers selected from primers described herein.

In an embodiment, the plurality is a plurality of primer pairs.

A further aspect is a probe that is specific for an allele.

In yet another embodiment, the primer or probe further comprises a covalently bound tag, optionally a sequence specific nucleotide tail or label. The primer or probe nucleotide sequence tag can comprise or can be coupled to a fluoresecent, radioactive, metal or other detectable label.

The primer or probe can also comprise a linker.

Yet a further aspect includes an array, optionally a species specific array comprising a plurality of nucleic acid probes attached to a support surface, each isolated nucleic acid probe comprising a sequence of about 9 to about 100 nucleotides, for example about 9 to about 50 nucleotides or about 18 to about 30 nucleotides, wherein the sequence is at least 9, 12, 15 or at least 18 contiguous nucleotides of any one of SEQ ID NOs: 1-600.

The probe can comprise a sequence that is just upstream of the SNP nucleotide, for example nucleotides 83-100 of any odd numbered SEQ ID NO: 1-600. In an embodiment, the array comprises allele specific probes (nucleic acids optionally labeled), for example wherein the probe comprises upstream sequence and the SNP.

In an embodiment, the array further comprises one or more negative control probes and/or one or more positive control probes.

A further aspect includes a kit comprising an isolated nucleic acid, primer, or plurality of primers and/or array described herein.

The kit can comprise various other reagents for amplifying DNA and/or using an array to detect a SNP such as dNTPs, polymerase, reaction buffer, wash buffers and the like. Accordingly in an embodiment, the kit comprises at least one reagent for an amplifying DNA reaction.

In an embodiment, the kit further comprises at least one reagent for a primer extension reaction.

In an embodiment, the set for any of the methods, sets, pluralities, kits, nucleic acids or arrays comprises at least 10, 20, 30, 40 of the SNPS in Table 4, 5 and/or 8.

The above disclosure generally describes the present application. A more complete understanding can be obtained by reference to the following specific examples. These examples are described solely for the purpose of illustration and are not intended to limit the scope of the application. Changes in form and substitution of equivalents are contemplated as circumstances might suggest or render expedient. Although specific terms have been employed herein, such terms are intended in a descriptive sense and not for purposes of limitation.

The following non-limiting examples are illustrative of the present disclosure:

EXAMPLES Example 1

Despite its cultivation as a source of food, fibre and medicine, and its global status as the most used illicit drug, the genus Cannabis has an inconclusive taxonomic organization and evolutionary history. Drug types of Cannabis (marijuana), which contain high amounts of the psychoactive cannabinoid delta-9 tetrahydrocannabinol (THC), are used for medicinal purposes and as a recreational drug. Hemp types are grown for the production of seed and fibre, and contain low amounts of THC. Two species or gene pools (C. sativa and C. indica) are widely used in describing the pedigree or appearance of cultivated cannabis plants. Using 14,031 single-nucleotide polymorphisms (SNPs) genotyped in 81 marijuana and 43 hemp samples, marijuana and hemp are found to be significantly differentiated at a genome-wide level, demonstrating that the distinction between these populations is not limited to genes underlying THC production. There is a moderate correlation between the genetic structure of marijuana strains and their reported C. sativa and C. indica ancestry.

To evaluate the genetic structure of commonly cultivated Cannabis, 81 marijuana and 43 hemp samples were genotyped using genotyping-by-sequencing (GBS) [5]. The marijuana samples represent a broad cross section of modern commercial strains and landraces, while the hemp samples include diverse European and Asian accessions and modern varieties. In total, 14,031 SNPs were identified after applying quality and missingness filters. Principal components analysis (PCA) of both marijuana and hemp (FIG. 1a ) revealed clear genetic structure separating marijuana and hemp along the first principal component (PC1). This distinction was further supported using the fastSTRUCTURE algorithm [6] assuming K=2 ancestral populations (FIG. 1c ). PCA and fastSTRUCTURE produced highly similar results: a sample's position along PC1 was strongly correlated with its group membership according to fastSTRUCTURE at K=2 (r₂=0.964; p-value=3.55×10⁻⁹⁰).

A putative C. indica marijuana strain from Pakistan that is genetically more similar to hemp than it is to other marijuana strains was identified (FIG. 1a ). Similarly, hemp sample CAN 37/97 clusters more closely with marijuana strains (FIG. 1a ). These outliers may be due to sample mix-up or their classification as hemp or marijuana may be incorrect.

These results significantly expand our understanding of the evolution of marijuana and hemp lineages in Cannabis. Previous analyses have shown that marijuana and hemp differ in their capacity for cannabinoid biosynthesis, with marijuana possessing the B_(T) allele coding for tetrahydrocannabinolic acid synthase and hemp typically possessing the B_(D) allele for cannabidiolic acid synthase [7]. As well, transcriptome analysis of female flowers showed that cannabinoid pathway genes are significantly upregulated in marijuana compared to hemp, as expected from the very high THC levels in the former compared to the latter [3]. The present results indicate that the genetic differences between the two are distributed across the genome and are not restricted to loci involved in cannabinoid production. In addition, levels of heterozygosity are higher in hemp than in marijuana (FIG. 1b , Mann-Whitney U-test, p-value=8.64×10⁻¹⁴), which suggests that hemp cultivars are derived from a broader genetic base than that of marijuana strains and/or that breeding among close relatives is more common in marijuana than in hemp.

The difference between marijuana and hemp plants has considerable legal implications in many countries, and to date forensic applications have largely focused on determining whether a plant should be classified as drug or non-drug [8]. EU and Canadian regulations only permit hemp cultivars containing less than 0.3% THC to be grown. While hemp and marijuana appear relatively well separated along PC1 (FIG. 1a ), no SNPs with fixed differences were found between these two groups: the highest FST value between hemp and marijuana among all 14,031 SNPs was 0.87 for a SNP with an allele frequency of 0.82 in hemp and 0 in marijuana (Table 1).

The average FST between hemp and marijuana is 0.156 (FIG. 3), which is similar to the degree of genetic differentiation in humans between Europeans and East Asians [9]. Thus, while cannabis breeding has resulted in a clear genetic differentiation according to use, hemp and marijuana still largely share a common pool of genetic variation.

Although the taxonomic separation of the putative taxa C. sativa and C. indica remains controversial, a vernacular taxonomy that distinguishes between “Sativa” and “Indica” strains is widespread in the marijuana community. Sativa-type plants tall with narrow leaves, are widely believed to produce marijuana with a stimulating, cerebral psychoactive effect while Indica-type plants, short with wide leaves, are reported to produce marijuana that is sedative and relaxing. The genetic structure of marijuana is in partial agreement with strain-specific ancestry estimates obtained from various online sources (FIG. 2, Table 2). A moderate correlation between the positions of marijuana strains along the first principal component (PC1) of FIG. 2a and reported estimates of C. sativa ancestry (FIG. 2c )(r ₂=0.22; p-value=9×10⁻⁶) was observed. This relationship is also observed for the second principal component (PC2) of Fig. la (r²=0.23; p-value=6.71×10⁻⁶). This observation suggests that C. sativa and C. indica may represent distinguishable pools of genetic diversity [1] but that breeding has resulted in considerable admixture between the two. While there appears to be a genetic basis for the reported ancestry of many marijuana strains, in some cases the assignment of ancestry strongly disagrees with our genotype data. For example Jamaican Lambs Bread (100% reported C. sativa) was nearly identical (IBS=0.98) to a reported 100% C. indica strain from Afghanistan. Sample mix-up cannot be excluded as a potential reason for these discrepancies, but a similar level of misclassification was found in strains obtained from Dutch coffee shops based on chemical composition [10]. The inaccuracy of reported ancestry in marijuana likely stems from the predominantly clandestine nature of Cannabis growing and breeding over the past century. Recognizing this, marijuana strains sold for medical use are often referred to as Sativa or Indica “dominant” to describe their morphological characteristics and therapeutic effects [10]. The results suggest that the reported ancestry of some of the most common marijuana strains only partially captures their true ancestry.

Materials and Methods

Genetic material and genotyping. The marijuana strains genotyped were grown by Health Canada authorized producers and represent germplasm grown and used for breeding in the medical and recreational marijuana industries (Table 2). Hemp strains were obtained from a Health Canada hemp cultivation licensee, and represent modern seed and fibre cultivars grown in Canada as well as diverse European and Asian germplasm (Table 3). DNA was extracted from leaf tissue using standard protocols, and library preparation and sequencing were performed using the GBS protocol published by Sonah et al [15]. SNPs were called using the GBS pipeline developed by Gardner et al. [16], aligning to the canSat3 C. sativa reference genome assembly [3]. Quality filtering of genetic markers was performed in PLINK [17] by removing SNPs with (i) greater than 20% missingness by locus (ii) a minor allele frequency less than 1% and (iii) excess heterozygosity (a Hardy-Weinberg equilibrium p-value less than 0.0001). After filtering, 14,031 SNPs remained for analysis.

Collection of reported marijuana ancestry. Reported ancestry proportions (% C. sativa and % C. indica) were manually obtained from online strain databases, cannabis seed retailers, and licensed producers of medical marijuana (Table 2). Ancestry estimates for 26 strains for which no online information was available were assigned.

Analysis of population structure and heterozygosity. Principal components analysis (PCA) was performed using the adegenet v1.4-2 package [18] in R v3.1.1 using default parameters. fastSTRUCTURE [6] was run at K=2 and K=3 using default parameters for hemp and marijuana samples combined (14,031 SNPs) (FIG. 1a,c ), and marijuana samples alone (10,651 SNPs) (FIG. 2a,b ). Heterozygosity by individual was calculated in R by dividing the number of heterozygous sites by the number of non-missing genotypes for each sample.

Identity by state (IBS) Analysis. Pairwise proportion IBS between all pairs of samples was calculated using PLINK. One outlier was excluded from this analysis, C. indica (Pakistan), because of its significantly higher IBS to hemp than all other marijuana strains (Labeled marijuana sample in FIG. 1a ).

To determine if the hemp population shared greater allelic similarity to C. sativa or C. indica marijuana, the mean pairwise IBS was calculated between each marijuana strain and all hemp strains. This analysis was performed at various minor allele frequency thresholds and the result remained unchanged.

Example 2 Selection of Cannabis Informative Markers

Nine reported C. indica and 9 reported C. sativa individuals were selected to form ancestral populations for the selection of genetic markers that are able to differentiate the two groups. Individuals were selected manually on the basis of both their position along the first principal component in FIG. 5 (actual genetic structure observed using 9776 SNPs), as well as their reported C. sativa or C. indica ancestry.

Selection of Ancestry Informative Markers (AIMs)

The top 100 highest F_(ST) SNPs were extracted and evaluated for their use in estimating genetic structure, which in the present case is being used as a proxy for C. sativa/C. indica ancestry given the unavailability of true pure C. sativa and C. indica populations. The same was performed between hemp cultivars and marijuana strains of Cannabis (FIG. 1a ).

Example Evaluation of AIMs for Estimating Population Structure

Assuming the first principal component of FIG. 5 is representative of population structure between C. indica and C. sativa type marijuana strains, a strain's position along the X axis (PC1) represents genetic similarity to each population. In the case of admixed individuals, the position could be representative of genomic contribution from the C. indica and C. sativa gene pools. For the purposes of this analysis, an individual's position along PC1 using 9776 SNPs (FIG. 5), is considered to be an individual's true ancestry. By projecting samples on to principal components computed using only the ancestral populations, additional samples can be added to the analysis without changing the relative positions of our ancestral strains in PC space and the centroids of the clusters can be used as anchors along PC1 for estimating ancestry. Because not every SNP will contribute equally to an individual's position along PC1, a subset of markers that will capture nearly all the variance accounted for by that component is selected.

First, the 2 highest F_(ST) SNPs are selected, and used to perform PCA using only the ancestral C. sativa and C. indica populations. The rest of the samples are then projected (n=63) onto those components, and their positions along PC1 stored. To determine the accuracy of this 2 marker panel, the Pearson's product moment correlation coefficient (Y axis, FIG. 6) was calculated between these positions and the positions calculated using the full set of 9766 SNPs. The next highest F_(ST) SNP was added to the panel and this process was repeated for all 100 highest F_(ST) markers. Accuracy is not improved within this dataset for marker panels of more than approximately 40 of the highest F_(ST) SNPs within this population (FIG. 7). Additional ancestry informative SNPs may provide greater accuracy in novel samples and can provide redundancy in the event of failed genotyping reactions.

Example 3 Weighting of SNPs:

To rank SNPs according to their ancestry informativeness, the fixation index (F_(ST)) according to Weir and Cockerham (1984) was calculated for each marker. This estimate ranges between 0 and 1, where a SNP with F_(ST)=1 has an allele found at 100% frequency in one population, and 0% frequency in another.

Willing, Dreyer, and van Oosterhout (2012) [21] describe the calculation as follows:

“At a single locus k, F_(ST) ^(W&C) is defined as

${\hat{F}}_{ST}^{\lbrack k\rbrack} = \frac{{\hat{N}}^{\lbrack k\rbrack}}{{\hat{D}}^{\lbrack k\rbrack}}$ where ${\hat{N}}^{\lbrack k\rbrack} = {s^{2} - {\frac{1}{{2n} - 1}\left\lbrack {{\overset{\_}{p}\left( {1 - \overset{\_}{p}} \right)} - {\frac{r - 1}{r}s^{2}} - \frac{\overset{\_}{h}}{4}} \right\rbrack}}$ ${\hat{D}}^{\lbrack k\rbrack} = {{\overset{\_}{p}\left( {1 - \overset{\_}{p}} \right)} + \frac{s^{2}}{r}}$

Here, s² is the observed variance of allele frequencies, n is the number of individuals per population, p is the mean allele frequency over all populations, r is the number of sampled populations and h is the mean observed heterozygosity.”

Example 4 Population Assignment

Population assignment can be performed if the novel sample has been genotyped for ancestry informative markers for which the alleles and allele frequencies are already known in the ancestral populations.

A test sample of a cannabis sample to be characterized is obtained. The test sample is genomic DNA and the genomic DNA is subjected to genotyping of at least 10 of the markers in Table 4 or Table 5 depending on whether it is desired that the ancestral contribution be determined or the sample be identified as marijuana or hemp.

An assignment test developed by Paetkau et al (23) and described in Hansen, Kenchington and Nielsen (2001) (24) can be used.

For each cannabis sample being assigned, the log-likelihood of it being derived from a specific population is calculated as:

$\begin{matrix} {\log \left( {{{\prod\limits_{l = 1}^{n}\; {p_{ij}^{2}\mspace{14mu} {for}\mspace{14mu} i}} = j},{{{and}\mspace{14mu} 2p_{i}p_{j}\mspace{14mu} {for}\mspace{14mu} i} \neq j}} \right)} & {{Equation}\mspace{14mu} 1} \end{matrix}$

where n denotes the number of loci, I and j denote the two alleles at the

h locus, and p_(i) and p_(j) denote the frequency of the

h and

th allele of the

h locus in the population being considered.

Calculations are made for each population using the loci and frequencies provided in Table 4 or 5, and the cannabis sample is assigned to the population in which it has the highest likelihood of belonging.

Example 5 Ancestry Estimation

Calculation of a novel sample's hybridization index (e.g. ancestry contribution) can be performed if the novel sample has been genotyped for ancestry informative markers for which the alleles and allele frequencies are already known in the ancestral populations.

Ancestry analysis can determine if the cannabis sample is a ‘pure’ descendant of a reference sample or reference profile or if it is the result of interbreeding between individuals from two different populations, i.e. an admixed individual or ‘intraspecific hybrid’.

Campton and Utter (1985) developed a “hybrid index” (25). The hybrid index can be regarded as a way of visualizing the relative assignment probabilities in an assignment test involving two parental populations. The hybrid index, I_(H), requires three samples (or a sample and two reference profiles), i.e. a sample or reference profile of each of the two possible parental populations and a sample of the group of suspected ‘hybrids’.

I_(H) is calculated as:

$\begin{matrix} {I_{H} = {1 - \frac{\log \left( p_{x} \right)}{{\log \left( p_{x} \right)} + {\log \left( p_{y} \right)}}}} & {{Equation}\mspace{14mu} 2} \end{matrix}$

where p_(x) denotes the likelihood of the multilocus genotype of an individual in population x and p_(y) similarly denotes the likelihood in population y, calculated as in equation 1.”

Example 6 SNP Discovery

Genetic material and genotyping. The marijuana strains genotyped were grown by Health Canada authorized producers and represent germplasm grown and used for breeding in the medical and recreational marijuana industries (Table 10). DNA was extracted from leaf tissue using standard protocols, and library preparation and sequencing were performed using the GBS protocol published by Poland et al [26] SNPs were called using the GBS pipeline developed by Melo et al. [27], aligning to the canSat5 C. sativa reference genome assembly (unpublished). Quality filtering of genetic markers was performed in PLINK [17] by removing SNPs with (i) greater than 20% missingness by locus (ii) a minor allele frequency less than 1% and (iii) excess heterozygosity (a Hardy-Weinberg equilibrium p-value less than 0.0001). After filtering, 9,123 SNPs remained for analysis.

Table 8 identifies the major and minor alleles identified in Cannabis sativa and Cannabis indica and Table 9 provides upstream and downstream sequence for each SNP. Table 10 provides reference information on the reported ancestry. FIG. 8 shows a PCA analysis based on whether the strain is reported as C indica or C sativa.

TABLE 1 Positions and allele frequencies of the top 50 SNPs by FST between marijuana and hemp calculated according to equation 10 in Weir and Cockerham (1984) [19]. SNP FST Between Non-Reference Non-Reference Position on Hemp and Reference Non-Reference Allele Frequency Allele Frequency Scaffold Scaffold Marijuana Allele Allele in Marijuana in Hemp scaffold13038 51303 0.865332249 C A 0 0.8158 scaffold25092 11841 0.85295301 A G 0.08333 0.9583 scaffold23837 26190 0.81783437 C T 0.04938 0.8605 scaffold152474 1505 0.813648101 C A 0.01282 0.7857 scaffold152474 1465 0.810651442 G A 0.03205 0.8214 scaffold13038 51162 0.805163299 C T 0 0.7436 scaffold5841 136325 0.782037623 A T 0.006329 0.7059 scaffold5876 22669 0.779767209 A T 0.175 1 scaffold764 75880 0.770853139 C A 0 0.7024 scaffold32076 9119 0.767411438 C A 0.01316 0.7143 scaffold7992 917 0.763602811 T A 0.006329 0.7073 scaffold118405 2916 0.761994625 C T 0.03125 0.7564 scaffold2418 77480 0.758065142 G T 0 0.6618 scaffold34829 1873 0.746880355 T C 0.1645 0.9535 scaffold38125 4641 0.743833337 G T 0.03704 0.7558 scaffold37469 74270 0.740257391 G A 0.1013 0.8611 C32100775 1618 0.736074476 T C 0.01316 0.6613 scaffold5190 41424 0.734073333 C G 0.109 0.869 scaffold5190 41454 0.734073333 G A 0.109 0.869 scaffold49917 1105 0.726261988 A G 0.08642 0.8256 scaffold4775 75747 0.719005761 T A 0 0.625 scaffold26152 15432 0.712320041 G A 0.05921 0.7571 scaffold5841 135056 0.712144097 G A 0 0.6429 scaffold5876 106401 0.711616024 A G 0 0.6395 scaffold5113 138895 0.711038199 A G 0 0.6111 scaffold5113 239777 0.710611128 G A 0 0.631 scaffold5841 135067 0.70853417 G A 0 0.6429 scaffold25099 7321 0.702374753 A G 0.05556 0.7439 scaffold14172 40875 0.702287484 A C 0.01282 0.5682 scaffold158332 502 0.702084439 A G 0.006173 0.6395 scaffold16869 149709 0.700892589 T G 0.1562 0.9024 scaffold114539 1119 0.695979272 C T 0 0.6111 scaffold3842 272682 0.69126068 T G 0.01266 0.6 scaffold60331 8510 0.690556532 G C 0.03425 0.6892 scaffold2360 22109 0.689941474 G A 0.07143 0.7639 scaffold72613 1728 0.689632536 G A 0.04321 0.7093 C32052717 309 0.688864374 A T 0.142 0.8721 scaffold71943 13435 0.685008651 C T 0.01852 0.6512 scaffold71943 13471 0.685008651 T C 0.01852 0.6512 scaffold128544 170 0.679301025 G T 0.01875 0.6316 scaffold98263 1069 0.677597364 T C 0.07407 0.7558 C32058675 292 0.673619414 A G 0.01852 0.6395 scaffold823 11824 0.673537258 C T 0.01299 0.6111 scaffold75287 5899 0.673496392 G T 0.04321 0.6905 scaffold16869 149730 0.671387324 C T 0.1562 0.875 scaffold3842 543149 0.670719701 C T 0.02469 0.6212 C32058613 508 0.67046277 T C 0 0.5588 C32058613 563 0.67046277 C T 0 0.5588 scaffold7146 70340 0.669199626 C T 0.1667 0.8889 scaffold23125 41276 0.669066022 G A 0.03846 0.675

TABLE 2 Sample names and reported C. sativa and C. indica ancestry of genotyped marijuana strains. Reported Reported Proportion Proportion Sample ID Sample Name C. Sativa C. indica Reference for Reported Ancestry P2_A01_M_0001 C. indica 0 100 Author D H (Afghanistan) P2_A02_M_0002 Ata Tundra 0 100 http://www.gorilla-cannabis-seeds.co.uk/seedsman/regular/ata-tundra.html P2_A03_M_0003 Big Bang 20 80 http://www.kindgreenbuds.com/marijuana-strains/big-bang/ P2_A04_M_0004 Big Bang 10 80 http://azarius.net/seedshop/greenhouseseeds/big_bang_autoflowering_greenhouse/ (Autoflowering) P2_A05_M_0005 Dr. Grinspoon 100 0 http://www.leafly.com/sativa/dr-grinspoon P2_A06_M_0006 Hash Passion 0 100 http://www.seedsman.com/en/hash-passion-seeds P2_A07_M_0007 Indian Haze 100 0 http://en.seedfinder.eu/strain-info/Indian_Haze/Seedsman/ (Haze Mist) P2_A09_M_0009 King Kush 30 70 http://grow-marijuana.com/strain-reviews/king-kush P2_A10_M_0010 Master Kush 5 95 http://sensiseeds.com/en/cannabis-seeds/whitelabel/master-kush P2_A11_M_0011 Master Kush 5 95 http://sensiseeds.com/en/cannabis-seeds/whitelabel/master-kush P2_A12_M_0012 Master Kush 5 95 http://sensiseeds.com/en/cannabis-seeds/whitelabel/master-kush P2_B01_M_0013 Master Kush 5 95 http://sensiseeds.com/en/cannabis-seeds/whitelabel/master-kush P2_B03_M_0015 Neville's Haze 75 25 http://www.leafly.com/hybrid/nevilles-haze P2_B04_M_0016 C. indica 0 100 Author D H (Pakistan) P2_B05_M_0017 C. sativa 100 0 Author D H (South Africa) P2_B07_M_0019 White Rhino 10 90 http://www.kindgreenbuds.com/marijuana-strains/white-rhino/ P2_B08_M_0020 White Widow 50 50 http://www.royalqueenseeds.com/122-white-widow.html P2_B09_M_0021 Chemdawg 50 50 http://www.tweed.com/collections/all-strains/products/donegal-chem-dawg P2_B10_M_0022 Vanilla Haze 20 80 https://www.barneysfarmshop.com/seeds/vanilla-kush.html P2_B12_M_0024 Sunshine 90 10 Author D H P2_C01_M_0025 NL5 Haze Mist 50 50 http://www.popularseeds.com/green-house-seeds/nl5-haze-mist P2_C03_M_0027 El Nino 40 60 http://www.kindgreenbuds.com/marijuana-strains/el-nino/ P2_C04_M_0028 Shark 25 75 http://www.weedyard.com/Strains/SharkShock.html P2_C05_M_0029 King Kush 30 70 http://www.wikileaf.com/strain/kings-kush/ P2_C06_M_0030 Dr. Grinspoon 100 0 http://www.leafly.com/sativa/dr-grinspoon P2_C07_M_0031 Exodus Cheese 40 60 http://www.gorilla-cannabis-seeds.co.uk/greenhouseseeds/feminized/exodus- cheese-feminized.html P2_C08_M_0032 Jenni 75 25 Author D H P2_C09_M_0033 Hawaiian Snow 90 10 http://www.kindgreenbuds.com/marijuana-strains/hawaiian-snow/ P2_C10_M_0034 GH Cheese 40 60 http://azarius.net/seedshop/greenhouseseeds/cheese_greenhouse_feminised/ P2_C11_M_0035 Kalishnikova 20 80 http://azarius.net/seedshop/greenhouseseeds/kalashnikova_greenhouse_feminized/ P2_D01_M_0037 Great White 25 75 http://www.kindgreenbuds.com/marijuana-strains/white-shark/ Shark P2_D02_M_0038 Strawberry 70 30 http://www.kindgreenbuds.com/marijuana-strains/arjans-strawberry-haze/ Haze P2_D03_M_0039 Himalayan 0 100 http://www.kindgreenbuds.com/marijuana-strains/himalaya-gold/ Gold P2_D04_M_0040 Ortega BC 0 100 http://www.leafly.com/indica/ortega P2_D05_M_0041 Atomic Haze 80 20 http://www.cannaseur.com/index.php/online-store/female-seeds/atomic- haze-female-detail P2_D06_M_0042 Domina Haze 85 15 Author D H P2_D07_M_0043 Rio 25 75 Author D H P2_D08_M_0044 Damn Sour 60 40 http://www.cannabissearch.com/strains/damn-sour/ P2_D09_M_0045 Nina 75 25 http://www.kindgreenbuds.com/marijuana-strains/la-nina/ P2_D10_M_0046 White Widow 50 50 http://www.royalqueenseeds.com/122-white-widow.html P2_E01_M_0049 Purple Sativa 70 30 Author D H P2_E02_M_0050 Bubba Kush 10 90 http://www.tweed.com/collections/all-strains/products/norfolk-bubba-kush P2_E03_M_0051 Delahaze 70 30 https://www.paradise-seeds.com/en/delahaze.html P2_E05_M_0053 Super Silver 75 25 http://www.tweed.com/collections/all-strains/products/leonidas-super-silver-haze Haze P2_E06_M_0054 Jack Herer 70 30 http://www.tweed.com/collections/all-strains/products/birds-eye-jack-herer P2_E07_M_0055 Pennywise 40 60 http://www.tweed.com/collections/all-strains/products/nova-pennywise P2_E08_M_0056 White Berry 25 75 http://www.harborsidehealthcenter.com/learn/white-berry-medical-cannabis.html P2_E09_M_0057 Skunk Haze 55 45 http://www.kindgreenbuds.com/marijuana-strains/skunk-haze/ P2_E10_M_0058 Durban Poison 100 0 http://www.leafly.com/sativa/durban-poison P2_E12_M_0060 Happy Face 25 75 Author D H P2_F01_M_0061 White Rhino 10 90 http://www.kindgreenbuds.com/marijuana-strains/white-rhino/ P2_F03_M_0063 Ice Cream 40 60 http://www.kindgreenbuds.com/marijuana-strains/ice-cream/ P2_F04_M_0064 C. sativa 100 0 Author D H (Thailand/Laos) P2_F05_M_0065 Diamond Girl 40 60 Author D H (Silver Pearl) P2_F06_M_0066 AMS 30 70 http://www.kindgreenbuds.com/marijuana-strains/ams/ P2_F07_M_0067 Lemon Skunk 60 40 http://www.kindgreenbuds.com/marijuana-strains/lemon-skunk/ P2_F08_M_0068 Arjans Haze #2 90 10 http://www.kindgreenbuds.com/marijuana-strains/arjans-haze-2/ P2_F10_M_0070 White Domina 0 100 http://www.headsite.com/white-domina-feminised-seeds-kannabia-446-p.asp P2_F11_M_0071 Blue Hell 20 80 http://www.cannabis-seeds.co.uk/medicalseeds/bluehell.html P2_F12_M_0072 Neville's White 80 20 Author D H Widow P2_G01_M_0073 Alaskan Ice 70 30 http://www.kindgreenbuds.com/marijuana-strains/alaskan-ice/ P2_G03_M_0075 Arjans Ultra 80 20 http://www.cannabissearch.com/strains/arjans-ultra-haze/ Haze #1 P2_G04_M_0076 Ken's Sweet 20 80 https://www.barneysfarmshop.com/seeds/barneys-farm-sweet-tooth.html Tooth P2_G05_M_0077 Neville's Haze 75 25 http://www.kindgreenbuds.com/marijuana-strains/nevilles-haze/ P2_G06_M_0078 Arjans Haze #3 80 20 http://www.kindgreenbuds.com/marijuana-strains/arjans-haze-3/ P2_G07_M_0079 Cupid 50 50 Author D H P2_G08_M_0080 Super Critical 25 75 http://www.wikileaf.com/strain/super-critical/ P2_G09_M_0081 Super Bud 35 65 http://www.kindgreenbuds.com/marijuana-strains/ed-rosenthal-super-bud/ P2_G10_M_0082 LadyBurn 1974 50 50 http://www.cannabissearch.com/strains/ladyburn-1974/ P2_G11_M_0083 Trainwreck 90 10 http://www.wikileaf.com/strain/trainwreck/ P2_G12_M_0084 C. indica 0 100 Author D H (Afghanistan) P2_H01_M_0085 Almighty 50 50 Author D H Whitey P2_H02_M_0086 C. sativa 100 0 http://www.seedsman.com/en/guatemala-regular-seeds (Guatemala) P2_H03_M_0087 C. sativa 100 0 Author D H (Laos) P2_H04_M_0088 La Riena de 100 0 http://www.seedsman.com/en/la-reina-de-africa-feminised-seeds Africa P2_H05_M_0089 Raspberry 70 30 http://www.kindgreenbuds.com/marijuana-strains/raspberry-cough/ Cough P2_H06_M_0090 Super Lemon 80 20 http://www.wikileaf.com/strain/super-lemon-haze/ Haze P2_H08_M_0092 Jocelyn 60 40 Author D H P2_H09_M_0093 Big Bang 20 80 http://www.kindgreenbuds.com/marijuana-strains/big-bang/ P2_H10_M_0094 C. indica 0 100 Author D H (Afghanistan) P2_H11_M_0095 Jamaican 100 0 http://www.leafly.com/sativa/lamb-s-bread Lambs Bread

TABLE 3 Sample names of genotyped hemp varieties. Sample ID Sample Name P1_A02_H_0001_2 Felina P1_A04_H_0002_2 Ferimon P1_A06_H_0003_2 Kompolti P1_A08_H_0004_2 Uniko B P1_A10_H_0005_2 Fedora 19 P1_A11_H_0006_1 Futura 77 P1_B01_H_0007_1 Fedrina P1_B04_H_0008_2 Suditalien or Sudi P1_B05_H_0009_1 LKSD or LKCSD P1_B09_H_0011_1 Bialobrzeskie P1_B12_H_0012_2 VIR 541 P1_C01_H_0013_1 VIR 569 P1_C04_H_0014_2 VIR 575 P1_C05_H_0015_1 Silesia P1_C08_H_0016_2 VIR 577 P1_C10_H_0017_2 Carmagnola P1_D02_H_0019_2 Zolotonsha 15 P1_D03_H_0020_1 Fedora 17 P1_D05_H_0021_1 K110 P1_D07_H_0022_1 Novosadska P1_D09_H_0023_1 Jus 8 P1_E01_H_0025_1 Delores P1_E03_H_0026_1 Petera P1_E05_H_0027_1 CAN 29/94 P1_E07_H_0028_1 CAN 37/97 P1_E10_H_0029_2 CAN 40/99 P1_F03_H_0032_1 CAN 39/98 P1_F06_H_0033_2 CAN 100/01 P1_F07_H_0034_1 CAN 18/95 P1_F09_H_0035_1 CAN 20/02 P1_F11_H_0036_1 CAN 24/89 P1_G01_H_0037_1 CAN 23/99 P1_G04_H_0038_2 CAN 17/95 P1_G05_H_0039_1 CAN 19/87 P1_G07_H_0040_1 CAN 22/88 P1_G10_H_0041_2 CAN 26/93 P1_G11_H_0042_1 CAN 16/94 P1_H02_H_0044_1 CAN 28/01 P1_H04_H_0045_1 Chameleon P1_H07_H_0046_2 Tygra P1_H09_H_0047_2 Carmen P1_H10_H_0048_1 Alyssa P2_H12_H_0096 Finola

TABLE 4 Positions and allele frequencies of the top 100 SNPs by FST between Cannabis Sativa and Cannabis Indica calculated according to equation 10 in Weir and Cockerham (1984) [19] Minor Allele Minor Allele SEQ SEQ Minor Major Frequency Frequency SNP Name ID ID Allele Allele FST (Indica) (Sativa) scaffold14566:24841 1 2 C T 1 0 1 scaffold2257:59436 3 4 A C 0.941 0 0.9444 scaffold123303:7086 5 6 A C 0.938 0 0.9444 scaffold21832:18317 7 8 C T 0.937 0 0.9375 scaffold10653:22776 9 10 C T 0.937 0 0.9375 scaffold34968:5203 11 12 C A 0.933 0 0.9375 scaffold41828:12391 13 14 T C 0.883 0 0.8889 C32084869:1171 15 16 A T 0.876 0.9444 0.05556 scaffold1342:67015 17 18 C T 0.876 0.05556 0.9444 scaffold5876:136612 19 20 C T 0.876 0.05556 0.9444 scaffold10653:22755 21 22 G A 0.868 0.05556 0.9375 scaffold65043:4386 23 24 C A 0.866 0 0.875 scaffold39548:5676 25 26 T C 0.866 0 0.875 scaffold39548:5703 27 28 A G 0.866 0 0.875 scaffold17605:9224 29 30 G A 0.866 0 0.875 scaffold94301:10558 31 32 C T 0.858 0.0625 0.9375 scaffold52608:15151 33 34 G A 0.857 0 0.8571 scaffold9110:12755 35 36 G A 0.845 0.8571 0 C32099389:1875 37 38 G A 0.835 0.0625 0.9167 C32076905:769 39 40 G T 0.825 0 0.8333 scaffold50412:1217 41 42 T C 0.825 0.8333 0 scaffold73281:3231 43 44 T C 0.825 0 0.8333 scaffold60591:9229 45 46 T C 0.825 0 0.8333 scaffold60591:9364 47 48 G T 0.825 0 0.8333 scaffold27976:11462 49 50 T A 0.825 0.8333 0 scaffold4591:18700 51 52 A G 0.825 0.8333 0 scaffold96873:16326 53 54 A G 0.817 0 0.8333 scaffold6777:12771 55 56 C T 0.816 0 0.8333 C31894837:130 57 58 A G 0.812 0 0.8125 scaffold1342:66883 59 60 C T 0.812 0.8125 0 C32035477:264 61 62 G A 0.811 0.8889 0.05556 scaffold6360:1717 63 64 T C 0.811 0.05556 0.8889 scaffold132623:4144 65 66 T C 0.811 0.8889 0.05556 scaffold72006:11851 67 68 T A 0.809 0 0.8 scaffold6742:34122 69 70 C T 0.807 0 0.8333 scaffold3108:8782 71 72 G A 0.806 0 0.8333 scaffold11225:9528 73 74 A G 0.806 0 0.75 scaffold11225:9539 75 76 T A 0.806 0 0.75 scaffold2579:59858 77 78 A G 0.803 0.8889 0.05556 scaffold5876:136559 79 80 T C 0.803 0.8889 0.05556 scaffold5876:136606 81 82 T C 0.803 0.8889 0.05556 scaffold23386:12397 83 84 A G 0.803 0 0.8125 scaffold93032:4944 85 86 A G 0.791 0 0.8125 scaffold94004:13663 87 88 A G 0.791 0.8125 0 scaffold26621:73038 89 90 C A 0.791 0 0.8125 scaffold26621:73058 91 92 G A 0.791 0 0.8125 scaffold62259:15201 93 94 C A 0.781 0 0.75 scaffold38801:13810 95 96 A G 0.768 0 0.7778 scaffold6550:117010 97 98 C T 0.768 0 0.7778 scaffold94863:28465 99 100 T C 0.767 0.1667 1 scaffold130551:553 101 102 T A 0.759 0 0.7778 scaffold21832:579 103 104 C A 0.759 0 0.7778 C32090201:1470 105 106 C T 0.759 0 0.7778 scaffold117639:1939 107 108 C A 0.759 0 0.7778 scaffold73281:2531 109 110 A G 0.759 0 0.7778 scaffold95390:2586 111 112 T C 0.759 0 0.7778 scaffold109105:3417 113 114 C T 0.759 0.7778 0 scaffold9670:13701 115 116 T C 0.759 0 0.7778 scaffold45478:20587 117 118 C T 0.759 0 0.7778 scaffold23700:29096 119 120 C A 0.759 0.7778 0 scaffold10732:30120 121 122 A G 0.759 0 0.7778 scaffold16969:31933 123 124 T C 0.759 0.7778 0 scaffold3884:40695 125 126 A G 0.759 0 0.7778 scaffold829:52127 127 128 A G 0.759 0 0.7778 scaffold6550:117004 129 130 G A 0.759 0.7778 0 scaffold27604:1398 131 132 A G 0.757 0 0.6667 scaffold125644:4761 133 134 G A 0.757 0.7778 0 scaffold16027:10666 135 136 C T 0.757 0 0.7778 scaffold2502:17437 137 138 G A 0.757 0 0.7778 scaffold2502:17515 139 140 C G 0.757 0 0.7778 scaffold70502:1951 141 142 C T 0.754 0.8571 0.0625 scaffold40620:28184 143 144 T C 0.751 0 0.75 scaffold40620:28194 145 146 G A 0.751 0 0.75 scaffold40620:28201 147 148 A T 0.751 0 0.75 scaffold118158:666 149 150 C G 0.74 0.1111 0.8889 scaffold41951:881 151 152 T A 0.74 0.1111 0.8889 scaffold95666:9974 153 154 T C 0.74 0.8889 0.1111 scaffold12645:86648 155 156 C T 0.74 0.1111 0.8889 scaffold6627:26364 157 158 T C 0.738 0.05556 0.8333 C32050599:443 159 160 T C 0.738 0.75 0 scaffold20861:14886 161 162 A G 0.737 0.7778 0 scaffold30119:28969 163 164 T A 0.732 0.8333 0.0625 scaffold2257:75397 165 166 T C 0.731 0 0.7778 scaffold46867:905 167 168 T C 0.73 0.7143 0 scaffold65132:21260 169 170 A T 0.729 0 0.75 scaffold94863:28441 171 172 C T 0.729 0.1667 1 scaffold94004:13590 173 174 T C 0.726 0.75 0 scaffold94004:13632 175 176 T A 0.726 0.75 0 scaffold39420:9067 177 178 T C 0.723 0.1111 0.875 scaffold42291:6484 179 180 C T 0.717 0.7143 0 scaffold23828:34435 181 182 G T 0.714 0.9286 0.1667 scaffold15017:4539 183 184 C T 0.714 0.07143 0.8333 scaffold16607:2589 185 186 T C 0.713 0.875 0.1111 scaffold27758:4907 187 188 G A 0.713 0.875 0.1111 scaffold20809:7695 189 190 G C 0.713 0.875 0.1111 scaffold36583:13571 191 192 T C 0.713 0.875 0.1111 scaffold36500:1728 193 194 T C 0.712 0 0.7222 scaffold36500:1740 195 196 C T 0.712 0 0.7222 scaffold36500:1749 197 198 T C 0.712 0 0.7222 scaffold153198:2269 199 200 A T 0.712 0 0.7222

TABLE 5 Positions and allele frequencies of the top 100 SNPs by FST between marijuana and hemp calculated according to equation 10 in Weir and Cockerham (1984) [19] Minor Allele Minor Allele SEQ SEQ Minor Major Frequency Frequency SNP Name ID ID Allele Allele FST (Marijuana) (Hemp) scaffold13038:51303 201 202 C A 0.865332249 0 0.8378 scaffold25092:11841 203 204 A G 0.85295301 0.08333 0.9571 scaffold23837:26190 205 206 C T 0.81783437 0.0375 0.881 scaffold152474:1505 207 208 C A 0.813648101 0 0.8049 scaffold152474:1465 209 210 G A 0.810651442 0.01948 0.8415 scaffold13038:51162 211 212 C T 0.805163299 0 0.7632 scaffold5841:136325 213 214 A T 0.782037623 0.00641 0.7273 scaffold5876:22669 215 216 A T 0.779767209 0.1646 1 scaffold764:75880 217 218 C A 0.770853139 0 0.7195 scaffold32076:9119 219 220 C A 0.767411438 0.01316 0.7353 scaffold7992:917 221 222 T A 0.763602811 0.00641 0.725 scaffold118405:2916 223 224 C T 0.761994625 0.03165 0.75 scaffold2418:77480 225 226 G T 0.758065142 0 0.6818 scaffold34829:1873 227 228 T C 0.746880355 0.1533 0.9524 scaffold38125:4641 229 230 G T 0.743833337 0.0375 0.7738 scaffold37469:74270 231 232 G A 0.740257391 0.1026 0.8611 C32100775:1618 233 234 T C 0.736074476 0.006667 0.6613 scaffold5190:41424 235 236 C G 0.734073333 0.1104 0.878 scaffold5190:41454 237 238 G A 0.734073333 0.1104 0.878 scaffold49917:1105 239 240 A G 0.726261988 0.075 0.8452 scaffold4775:75747 241 242 T A 0.719005761 0 0.6429 scaffold26152:15432 243 244 G A 0.712320041 0.04667 0.7794 scaffold5841:135056 245 246 G A 0.712144097 0 0.6585 scaffold5876:106401 247 248 A G 0.711616024 0 0.6548 scaffold5113:138895 249 250 A G 0.711038199 0 0.6111 scaffold5113:239777 251 252 G A 0.710611128 0 0.6463 scaffold5841:135067 253 254 G A 0.70853417 0 0.6585 scaffold25099:7321 255 256 A G 0.702374753 0.04375 0.7439 scaffold14172:40875 257 258 A C 0.702287484 0 0.5952 scaffold158332:502 259 260 A G 0.702084439 0 0.6548 scaffold16869:149709 261 262 T G 0.700892589 0.1456 0.9 scaffold114539:1119 263 264 C T 0.695979272 0 0.6111 scaffold3842:272682 265 266 T G 0.69126068 0 0.6207 scaffold60331:8510 267 268 G C 0.690556532 0.02083 0.7083 scaffold2360:22109 269 270 G A 0.689941474 0.05797 0.7857 scaffold72613:1728 271 272 G A 0.689632536 0.04375 0.7262 C32052717:309 273 274 A T 0.688864374 0.1437 0.8929 scaffold71943:13435 275 276 C T 0.685008651 0.01875 0.6667 scaffold71943:13471 277 278 T C 0.685008651 0.01875 0.6667 scaffold128544:170 279 280 G T 0.679301025 0.01266 0.6316 scaffold98263:1069 281 282 T C 0.677597364 0.06875 0.7738 C32058675:292 283 284 A G 0.673619414 0.00625 0.6548 scaffold823:11824 285 286 C T 0.673537258 0 0.6286 scaffold75287:5899 287 288 G T 0.673496392 0.04375 0.7073 scaffold16869:149730 289 290 C T 0.671387324 0.1456 0.8718 scaffold3842:543149 291 292 C T 0.670719701 0.025 0.6406 C32058613:508 293 294 T C 0.67046277 0 0.5758 C32058613:563 295 296 C T 0.67046277 0 0.5758 scaffold7146:70340 297 298 C T 0.669199626 0.1688 0.8857 scaffold23125:41276 299 300 G A 0.669066022 0.02597 0.675 scaffold2418:77508 301 302 A C 0.66841944 0 0.5758 scaffold12000:86305 303 304 T G 0.668293303 0.06494 0.75 scaffold24181:60784 305 306 T G 0.665305819 0.02985 0.7083 scaffold26621:72993 307 308 G C 0.66089327 0.01493 0.6389 scaffold6391:16360 309 310 T C 0.658649381 0 0.5952 scaffold88759:12655 311 312 A T 0.656740474 0.1824 0.9091 scaffold37469:74336 313 314 C T 0.65627789 0.2062 0.9405 scaffold12000:86310 315 316 T C 0.655527354 0.06494 0.7375 scaffold6143:103796 317 318 G A 0.651968566 0.00625 0.5976 scaffold33135:78155 319 320 A G 0.648604326 0.1 0.7976 C32058675:317 321 322 G A 0.644770212 0.025 0.6667 scaffold1976:5193 323 324 G A 0.644158158 0.01333 0.569 C32098343:2061 325 326 T G 0.643381806 0.225 0.9405 scaffold158089:295 327 328 A G 0.642783505 0.01316 0.6053 scaffold17267:6243 329 330 T C 0.641890359 0.7372 0 scaffold491:22100 331 332 A G 0.640380595 0 0.575 scaffold121522:9070 333 334 C A 0.634641583 0.1899 0.9167 scaffold24615:2202 335 336 G C 0.63300106 0.0125 0.5952 C32052323:699 337 338 A G 0.62920484 0.00625 0.5789 C32052323:711 339 340 C T 0.62920484 0.00625 0.5789 scaffold14925:8868 341 342 G T 0.626191251 0 0.5714 scaffold133681:2742 343 344 A T 0.624116063 0.03125 0.631 scaffold9639:84033 345 346 G C 0.623460076 0 0.5488 scaffold61482:2893 347 348 T C 0.623250917 0 0.5714 scaffold30395:12115 349 350 C T 0.622098398 0.2562 0.95 C32064647:1071 351 352 T C 0.621516382 0.06757 0.6935 scaffold2452:1249 353 354 C T 0.62106722 0.1709 0.869 scaffold11436:6161 355 356 G A 0.619484202 0.02597 0.5833 scaffold4156:16965 357 358 G A 0.61693912 0 0.5476 scaffold43435:8325 359 360 T C 0.616228929 0 0.4783 scaffold11297:60144 361 362 T A 0.615278463 0.7063 0.0125 scaffold51841:4904 363 364 A C 0.612402044 0.02083 0.5811 scaffold38015:40961 365 366 A G 0.611084671 0.01899 0.5789 scaffold16206:63417 367 368 A G 0.607275173 0 0.5366 scaffold13781:319 369 370 T C 0.603383314 0.02564 0.6143 scaffold27023:20610 371 372 T C 0.603215502 0.025 0.5952 scaffold4618:83522 373 374 T C 0.600515019 0.03289 0.6094 scaffold111383:2928 375 376 G A 0.598738059 0.0443 0.6341 scaffold29335:25795 377 378 C T 0.598716088 0.1447 0.8 scaffold122455:2010 379 380 C G 0.597062664 0 0.5238 scaffold13362:101120 381 382 A C 0.595795194 0 0.5238 scaffold38557:23764 383 384 A T 0.595178777 0.01923 0.5 scaffold38557:23794 385 386 G A 0.595178777 0.01923 0.5 scaffold50091:2544 387 388 G A 0.595100084 0.006494 0.5 scaffold16614:72706 389 390 A T 0.594825378 0 0.4483 scaffold4877:4542 391 392 A G 0.593079588 0 0.5 scaffold65894:5390 393 394 A T 0.590807732 0 0.4857 scaffold90107:10791 395 396 T C 0.590194744 0 0.5122 scaffold68873:1704 397 398 A T 0.586079433 0 0.4875 scaffold3842:188176 399 400 C T 0.584333199 0 0.5161

TABLE 6 Upstream, Allele and Downstream sequences for SNPs from Table 4 SEQ SEQ SNP Name ID Upstream Sequence Minor Major ID Downstream Sequence scaffold 1 CAGATCCTAAATATGCTGATATTATTCTTTTA C T 2 ATAAGGAGTTATTATTATTTGTTTTGGGTGCATTGCTG 14566:24841 GAGAATTATGCAGCATTTCAGAATAGGTACAT AGTAGAAGCAGTTTCATGCAGCTTGTATGACCTAGCCA ATTTCATTCTTTTATTTTTTCTCCTGTATCTT ATGTTGTGCCTACCCTAGCCAAGT TCAT scaffold 3 CAATAAGACTTTCGATCGCTCTTGGTGCTGCA A C 4 AATGGGGTATTGAGGTTTGAAGAATTCTTTCATATGAA 2257:59436 CGAGGCAAGATTTCTATATTTGATATTGGCTT TCTGCAGGATTAACTTATCTTCACACATATGCCGGCTG GTCCCATTTGACAATTTTCCATTAAAATGGCT CGTTATACATAGGGATGTGAAATC GATG scaffold 5 TCCTCGATTGTTGAAGGAATTGTGGGGAGGCC A C 6 AGCAAACTGCAAGTTCTTGACAGTGTACTGAGGCAACA 123303:7086 TGCTTTGCGCTGCTGCTGGGCCCATGATAGTT CAAAGTGCAATTGTCAATTATGATCTGGAAGAGAAAGG TTTGCTGTAGTTTCACATTTTCTGGTTCAACT TTCGCAGCAAAAGACGCAACTAGA GTGA scaffold 7 CTGAAGCCAGGACAATGCAGCCAGCCAGTAGT C T 8 GGGCAAAGTTTGACGAGCCAGTCTAGCCAATTCGGAAA 21832:18317 GAGTATCATCATCAGTATGTTGTTGCTGTCAA TAACTCAGATTATAGTCCAAGTTTTTGTAGAGGCTCTC TGGCATGATGGACCCGAGTCCACGGAAGAGTT CTACAGCAGCATATGCAATGGAGA CAAG scaffold 9 CCATCATGAAATTCCCTTACCCTGGTGCCTTA C T 10 GACCGACTTGAGCTCCTCACAATGTGGCGCTTTCTACC 10653:22776 ACTGCTCTGCAGTATTTCACTAGTGCTTTTGG TGCTGCTGTTATATTCTATCTTTCCCTTTTCACCAATA GGTCTTCATTTGTGGATGGCTTAAGTTCATTG GTGAGTTGCTCCTTCATGCCAATG AGCA scaffold 11 CCCATGGAAACAAAAGTTCCCTGATATCAAAC C A 12 ACAAGTACTGACCTCAGGAGTTCCAAGAACCCAGTCAC 34968:5203 AGTGAAAAACTTTAGCACAACACAGCAGCATA GGATGTGATCACAAGCAGAGCTGGCAGCAGATAAAGCA GATATCGATAAGGAAACAGATTAATTGAAAAG CTTGATAGCTTACGAGCTTTGATA AAAA scaffold 13 AACCATTCATCTTCTTATCACTGCTGCCATTT T C 14 GTATAGGCCACACAAACCAAAAGATTAGCCTTGTTGTT 41828:12391 CTTGTTTGAATGTCATAAATTTTGGATTGGCA TTTGGCAGTAGCTTTCATGACTTTCTCAGCAGCAACTC GGATTCTTGAATAGCATGAACGATCTCATCAC TCACAGGCTCATTCAACAGTTTCA ACGA C32084869: 15 AATGGTTCCTCAATCTTCAAATCATCAGAAGC A T 16 CCCAAGGCCAAGTTCCACCTGTTTCATCAGGCCATGCA 1171 TCCTTGTTAGCTCGACTCTTCCTTCCACGAAG TTATCAACTTCCCAACAAGTTCCAGTGGCAGTTATGGG CAGCTCCATCAAATGCCTTCTCATTCAGATAA TCCCAATCACCAGCAGCTGCAGTC TAGC scaffold 17 CGTACCGTTCATTGTCTTTAGCTAACGACGCC C T 18 AGGCATAGGATTGGCTCATTGGCAGCAATTGGGGGTAA 1342:67015 AATGAAGCAGCAGCATCCGATCGTTCTTCCAA GCCGAGGTACTCGTCGTCTCGATCGCAGGCAGAGGCAG TGACCCCGTGTAAAGAATTGCTATCTGTTCCC AAACCCGAAGGAGCCAAGAGACAT ATAT scaffold 19 GCTCCGCTGCTGAAGATGTTTCCAAACCTGCA C T 20 TGCTGCTGAGTTTCTTTTTCATTAGTTGAATTAATGTA 76:136612 CACCAAGGAGTCTCTCGTATCCCCTGATGAGC TCTACAAACTATTTGTTACTGCTAAAAGCTTATTGTCT 58 TTGGTCCTTTTCAGGTAAAACTATCTTGCTCA TTAACTTATTATCACATCTATACT TCAT scaffold 21 TCTCTATAATCAACAAATGGGCCATCATGAAA G A 22 TGGCTTAAGTTCATTGAGCATGACCGACTTGAGCTCCT 10653:22755 TTCCCTTACCCTGGTGCCTTAACTGCTCTGCA CACAATGTGGCGCTTTCTACCTGCTGCTGTTATATTCT GTATTTCACTAGTGCTTTTGGGGTCTTCATTT ATCTTTCCCTTTTCACCAATAGTG GTGG scaffold 23 CGCGAAATAACATTCTCACCTTCTCCTCTCTC C A 24 ATCGAACACGGAATTCGCAAATACGGTGATTCGATCAA 65043:4386 GCCACCGCTGCTGCCGCTGTCGCATACGTTTT TAACGTTTTCGTTCACATTAAGCAAACCGGTGTTGCTG TCTCTCCTCCGATGATGATCGTGATCATAAGG CTTCGGTTCTCTGGCAATCGCTTA CCGC scaffold 25 AATAAAACATGAGCTTCTTGATATTCTCACTA T C 26 GATCGCTCCAGGTAAAGCCTGCCTCTGTATGCAGCCAA 39548:5676 AGTTTGGGTAGTGGCATAGTCTTTGGAGAAGC GTGAGCATAATAAACTGGGGGAACCAAAGAAACTGGTT AGCTCGAGAAAGTGAGGAAATAGTACTTTTGG TAGTACACCTTACGTATGTATAAC AGTC scaffold 27 CACTAAGTTTGGGTAGTGGCATAGTCTTTGGA A G 28 TATGCAGCCAAGTGAGCATAATAAACTGGGGGAACCAA 39548:5703 GAAGCAGCTCGAGAAAGTGAGGAAATAGTACT AGAAACTGGTTTAGTACACCTTACGTATGTATAACAAA TTTGGAGTCCGATCGCTCCAGGTAAAGCCTGC GATTGTACACCAGTTTCTGTAGTT CTCT scaffold 29 TACCATTTTCTTGCCCACAGGTTATTTTGCTG G A 30 TTCCAGGATATTCCTTTGTGCCATTTAGTAAAGTGAGT 17605:9224 CTATCCTTGCGTGGTTGTGGCCCACTCTGGCC CTAAAAGCAATGCTTATCTTTAAATATGGTATCTGGTG AAATCGGTTATCCTCATCAACAGTGCTGGAAA CAGCTGCTGACAACTGAAAGCTGT TGTC scaffold 31 TCAAGAGTTGGTTAGAAATTTATAACATACCA C T 32 GTTGATGAAGTTTTTCGGCTCACATCTTTACCTGGCTG 94301:10558 GAAGCAGCAGAAAATGCTGTACCGCTTCTTTT AGAGCCAGTTGCAGCATCTGTTCCTCCTTCACGTTTTT CTCAGCATCATGATGGTCTTTTGTAGTTTTTC GTCGAGCTTGTTCAGCCATAAGCT CAGG scaffold 33 CTAGCAGCTTCAAAATGGGTTTCTTTCTTTGG G A 34 CCACCAACCAATTCAGCAGCCATATTGATCAATGACAA 52608:15151 AACAGCTGGGATATGTCCTCCGAGGCCAATCT AAGTAACAAGTTCTTTGTTGAATCTGTGTAGGGGTTAC GTCAAACAGAACTTGAAGTGAAGCAGAGAGCA GGATGAGAATGAAGAAAGAAAGAA AAGC scaffold 35 CCCAAAGAGTTTGGTTATTTCCTAGTGTTACG G A 36 GTTTGTGAAGTGGGACCACTATTTCCTGCAGATGAAAC 9110:12755 ACTGTTGGAAAGGCCCTGTCTATTGTGGTGGC AACCGTGATCCCCTTTGATGCTGCATGGAAGGACCCAA TGCCACAGTTATGAGCCATGGTGCAGTGTTTG TTGCAATTGTGTCACGCAGATCAA AAAT C32099389: 37 TTGATCTACTGTTGCAGAACATGTATGCTCAG G A 38 CCACCTCCTATGGGGGGAATGGGAATGCCTCCAATGCC 1875 TTGCTGCCTCTTGCTTTGCCTGCCCCACCTAT ACCCTATGGCATGCCACCCATGGGGAGCAGCTATTGAG GCCGGGAATGGGAGGACCAGGAATGGGAGGCT ATGTATCAGGACTACGAGTTGTGA ATGC C32076905: 39 CTGACAATATAGCAATGCTTCATTAAATCTCA G T 40 CAAAATTCAAACCACAAGATCACTCTAACAAGTCACAA 769 TTATTACAAATACACTCATAAGCTCATCAATA CAAACACATAAAAGCATCAACTCTAGCAGCACCACCAC TAGATAATAGATATAGTAAGATACAAGCTGCA CACCAAACCAAGGCATCATCCCGA ATAC scaffold 41 GACTAAGCCTCAACTGGGTTTGGAAGAATTTT T C 42 TTAGGGAACCCAGTGACCTCGAATTCTTCAGACTCTGT 50412:1217 GACCATGAATCTGAACCGTCGGCTGCTCTCAA TTTCCGGTGAGGGAGTTCGTTCCAGATAGAAATGAAGG AAAGTAATGTAACTGAGAACGATGGAACCGGC CTGCAGAGCCGTAAGCGCCAGAAG ACCG scaffold 43 ACAAGAAGAATAGAAAGGCTGCTCTTACTATT T C 44 ACTTACTGCAAGCTGCTTGATGAGGTGAACAAAGAGAG 73281:3231 TTCTATGCCTTGGCCTTGGCTGAAGCTCTGTT TGAATTGGGAGGAGCTTCTGGTATGGTTTCAATCAGAA GTTTCTAATGGAGAAAGCTTATTGGGAATGGA GGTTCTTCTATGATGCCTATTCGA AGGT scaffold 45 CCAATTCCGCCACTGCTCCACTGCTGCTTGCT T C 46 GTTTCAGCATCATTACCATTTAATTTATCCTCTGGTAC 60591:9229 AGATTCTTCTCAGATGAGCGCTCAATCTCTTT TGGGCTGCTGTCTGGACCCCATTCTGATGAGTCTTTAA TGACAAAGATCCACCAAGCTCAGGCTTATCAT CATCTGCTTCAACTTCATGCGAGG CACC scaffold 47 GTACTGGGCTGCTGTCTGGACCCCATTCTGAT G T 48 GTTTCTAAACTAGCTGCAGTAGCATCCATTTGATCCAC 60591:9364 GAGTCTTTAACATCTGCTTCAACTTCATGCGA AGTTTCCAAGGAAGATCCAGATCTATTTATAATTCCAC GGTAGATGTAGATACCACAGATTCTGACATAG CAGTGAGGGGTGCATCCACATCAT TTTC scaffold 49 TCCATTGCAAAAACTACCACCATGGCTCTGAT T A 50 GATCAGAAGATTTATGAGTTGCTTCTTCAGAAAGTTGG 27976:11462 CAGCAGCAGCAAAAGAGCTAGGCTTCACTTCC TAACCTTGTTCCGAGTGTTGACTTGAGGTATTTGCTGC TCCACAAGATCAAACTCTTTCTTCTCTTGCTT AAATGGAGACTTCTCTCGCTGGCT GGTT scaffold 51 AAGCAGCATGGCGGCGATACAGTAAGAAAAAG A G 52 CCTAGTTTAGGTGCCACCATTTATGCTTCACGCTTTGC 4591:18700 CTTGAAGAGTCTCTTAGGGAAGAGGAGAATAG TGCAAACGCACTGCGTGCCATAAGGCGTAATAGTACAC GTTGCAGGATGCGTTGGCCAAGGCCGGGGCGA GTAAAACAAGGATGCCCGAAAGAA GCTC scaffold 53 AGGAGGCAACGGACTCTTCAACTTAGCAGCAG A G 54 AAGATTTCTGCTTCCGCGGATGTCGGATCTTGGCGGTG 96873:16326 CGGAAGGCGAGGGTTTAGGAATCGGAGGCAAG GTGCTGCTAGGGTTTGGAGATGGCGGAGGTTCCGTCTC GAGTTTGGATCGGCATAGGGCGGAGCATTCTC TCTCAAGATGTTATTTCTTGGCTG CTTG scaffold 55 ACCATTATGCGGTGTGTGCAAATTCGAATTGC C T 56 CTTCTTCATCTTCAGAACTCTCATCATCATCCTTGAAA 6777:12771 TCTCCCCATCTGAGTAGTCTGATATCAAGTGA ATTGACCCTGGTGTTAATCTTTTGTTTTGTTTTGAGCT TCTGATGGACTTCTTGTGCTGCTATCTGAACC GTTCAAGATTTCTCCATTGTACTT CACC C31894837: 57 ACTTCGGCTCTAGGCAGCCCTGCGCTTCGCAT A G 58 GGGCTGCAAGAGTAGAAGTCTTCAGCGATTCACAGTTA 130 TCCTAGCCTCAAACAACGAAGCCGAGTATGAA GTGGTCAATCAAGTGTCGGGGGAATACCAAACGCGTGG GCCCTAATTGCAGGACTAAAGTTATCAAAGGC AGAAAAAATAGCCGCTTACGTAGC CGTA scaffold 59 TGTGTTCAACGCTTTCCGGGTCACGCCCCAGA C T 60 GCCACCCCACCTTCCTCAATAATAAGCTTACCGTACCG 1342:66883 CGCCCAATTGCCGTGGCAGCATTCTCCTGACC TTCATTGTCTTTAGCTAACGACGCCAATGAAGCAGCAG TTCCATTCGGCCTTCTTTTGCCAATTTCAGAA CATCCGATCGTTCTTCCAATGACC GTGG C32035477: 61 GAGAAGAGAAATTATCATATGCCACCATGAGC G A 62 GCAAACAGTGCTTGTTTCTCCCATTCGTTTCGAACATT 264 AAAACCGCAGCCTCCTTTGCGAGGATAGAATT TAGCATGGTATTATCACTAGCAGCTTTTTTGGAAAAAC TTCTACCGAGAGAGTTTTGTCGGTCGCTTTCT TAAGGAAATACTTCAAGATGGCGA CCAT scaffold 63 ACTTGGCAATGTTAGCAGCCTGGTCCAGAGAA T C 64 TCAAGGTCAATGGACTCCAGAGCAGCCTTAACCATGGC 6360:1717 CTAGAGAGCAAGGGATGGAAGCATATATGGTC TAGGACTGAGGTTCTCAAGGGGCATGGATCCGAAGATG CACAATACCAAGCCGGGGATGACTGCCACTGT GTTGTGGATCCAACTTGGAAACAA GCAA scaffold 65 GTAAATGCAGTCCTTGTGATTGTTGTTGTTGT T C 66 CGACCAAATTGCTGTAAAAAGAAGTCATGCAACAGAAG 132623:4144 AAATGCCCGTCGTGTTTCAGTTGCTCGTTACC TTGTTGCTGCCTATTCCCTACTTCTTGTTGTTCATGCC AAAATGGCGTTGCCCTCGTTGTTCATGTTCGT CTGATTGCCCCTCTTGCAGATGCA GTCC scaffold 67 ATTGCTCTAGGGGCAGCCCGAGGCTTAGCTTA T A 68 TGACTTTACACCTAAGGTCTCAGACTTTGGATTGGCCA 72006:11851 TCTACATGAAGACTCCAATCCACGAGTGATTC GAGCAGCATTAGACGGTAACAGACATATCTCAACACAT ATCGAGATTTCAAGTCCAGCAACATCCTGTTA GTTATGGGCACTTTTGGGTAAGGA GAGC scaffold 69 AAAAAGTTGCAGCGGCAACAAAAGGTCTGTGT C T 70 GGTGGGTTGTTGGAGCCAATTGAGTATATTTCAACGGA 6742:34122 TGGGATTGAGAGGCTTTGAGAGAAGAGACCCT GGAAGTGTCGGAATCGGAGTCGAAAAAGGCGATGGCTG CGAGGGAGAAACCCACGAAGACTGAGGAGCTA CGAACCGGTCCAAGGCCGTGACTG GGTT scaffold 71 AGATAAAAGTCGCTCATTCTGAACCTCTTCCT G A 72 ATTCTCTCTTAGCTTGTGATGCTTTTACTTCTTCCTCT 3108:8782 CTAACGAAGCTGCTTTTAAGAGCAAGGTGTTG GCAGCTTTCTTTGATTCAGTAGCAAGAACCATCTTTAT ACCTCATTTTCAACTACTCTCAATCGAGACTC TTGCAGCTCCTGCAAATCCATTGC TGCC scaffold 73 AAGCAAATTAACAACCTGCTTATCAACCAAAC A G 74 AGGCTCCACTAGCAATTGATCTTCTTGCACCCTTCCTC 11225:9528 CCGGATGAGTAGTGACTACATAAGGGTTATTA ACTAAGTCTTGAGCAGCCCATATACTCCGCCAAATAAA TCATGGGGCAGCCACGGGTCATTTAGAATGCT ACTAGGATTATTTCCTAACTCAGC AACC scaffold 75 CAACCTGCTTATCAACCAAACCCGGATGAGTA T A 76 GCAATTGATCTTCTTGCACCCTTCCTCACTAAGTCTTG 11225:9539 GTGACTACATAAGGGTTATTATCATGGGGCAG AGCAGCCCATATACTCCGCCAAATAAAACTAGGATTAT CCACGGGTCATTTAGAATGCTAACCGAGGCTC TTCCTAACTCAGCATCAAGAAAGG CACT scaffold 77 TGCCGGATTTAGTGTGTAATAAAGACGAATCG A G 78 TTGAGGCTTAAACTCATCACTGAGCCTGCTGAGACTGC 2579:59858 AGCAGCTTTGGGTTCAAGAATTTGATGGAGAC TTCGTCGTCTCAGCTTCAAAATATGGCCATTAGAGTTG TTTCTGGGTTGACGTTCAAGAAGCTGAAGAGA AATTGAGGAATGGCTGCGTCGGAT GACC scaffold 79 GCACTTCCATTTACTTGGCCTCAGGCAAAATA T C 80 GTATCCCCTGATGAGCTTGGTCCTTTTCAGGTAAAACT 5876:136559 TACCAGGAAGAGAAACATCTAGCTCCGCTGCT ATCTTGCTCATCATCTGCTGCTGAGTTTCTTTTTCATT GAAGATGTTTCCAAACCTGCACACCAAGGAGT AGTTGAATTAATGTATCTACAAAC CTCT scaffold 81 CATCTAGCTCCGCTGCTGAAGATGTTTCCAAA T C 82 ATCATCTGCTGCTGAGTTTCTTTTTCATTAGTTGAATT 5876:136606 CCTGCACACCAAGGAGTCTCTCGTATCCCCTG AATGTATCTACAAACTATTTGTTACTGCTAAAAGCTTA ATGAGCTTGGTCCTTTTCAGGTAAAACTATCT TTGTCTTTAACTTATTATCACATC TGCT scaffold 83 CTAGTTTTAAGGATGCACAGTGGCTCCTCATC A G 84 ATAAATGACTTCAATGAGTACTATCTTAGTGATGGTGT 23386:12397 CAGAAAGCTGAAGAGGAAAAGCTTCTTCAAGT TAGTAAGTCTGCTCAACTGTGGAATGAGCAGCGAAAGT GACTATTAAGCTGCCAGAGGAGAAACTAAATA TGATATTGCAGGATGCTCTTTTTA AGTT scaffold 85 TGCAGCCCATTGTTGAGATGAATGAGATGTTA A G 86 AAGCAGCAACTTCTGTGATATCCAGTGGGTTTACTAAA 93032:4944 CATGCTTGAAGTTATGTTGATGTCTCATTTCT ATAGCGCCAGCACCGAGTGAATTTACTGCACCTGCACA CTTTCCTTAGCTATCATAGTCAAAGCATCACC CTAAATTTAAATGGAATAAACAAG AATG scaffold 87 TGTTAACAGCATCAGCAGCAGCAGCAGTATTA A G 88 CCAATATGGTGGAGCTGCAACATGGGGATTAGTCAGAC 94004:13663 TCCCTATTTCGTAAGGAACAAGGACGCCACAT ATAGCCAATTCCTTAATCCACCTCAATGAAAAAGAAAA ATATGTTACAGGAGCGATCGGCTTAGAAACTG GGACAGTAACTAACCATTGCATTA GTGC scaffold 89 ACGACGCCTACTACCAATAACCCAAATAGGGC C A 90 TACTACTACTACTACTACTACTACTACTGCTGCCTTCT 26621:73038 AGCAAGGATGATGATGATGACCACACAATCCT TCAGGGGTAGCACCATGGTGGATAAGCTAATCAAGGCC GCTCCCCAACACTCTCCAGACCACCCAACACA AGAAGATCATCATCAACAACACCT TCCA scaffold 91 CCCAAATAGGGCAGCAAGGATGATGATGATGA G A 92 CTACTACTGCTGCCTTCTTCAGGGGTAGCACCATGGTG 26621:73058 CCACACAATCCTGCTCCCCAACACTCTCCAGA GATAAGCTAATCAAGGCCAGAAGATCATCATCAACAAC CCACCCAACACATCCAATACTACTACTACTAC ACCTACCTACATATTATAACACAA TACT scaffold 93 ATGATGATTTAAAATGCATTAACTTCACATCC C A 94 CTCGGAAAAGGCTGCAAAAATGATAATCATAACTAGCA 62259:15201 CAATATTTCTCACCAACCCATAGACTCATAAC TAAAATATTGATCTTAATTCATAACTAAACCATATATT TTTAGCCTTTCCCTCTAAATATTGGATTGCAA TATAGAATCAAAACTTTTCAAACA ATTT scaffold 95 CAAAACCATCGCCGGAGAGAGAGAGGTTGTTT A G 96 AGGCAATCATGGAAGAGGAGGCGGAGAGTGGCGGCAGC 38801:13810 TCAGCATCTCGCTCAGCCTTGTTGAAGGCATT TGTGGTTGGGACCACCGATTGCTTTTCCTGTACAATCT GGAGGCGATGAGGATGGAGGCGTCGCAGCCTT GCCGTACGATGTCGGGGAATTTCG CGAC scaffold 97 TCGCCTTACAGGCTTTACTTGCACAGTCAAAG C T 98 CTGATTGTTGAGAAGTTTTTGTACTCGTGAAATAGAAG 6550:117010 ACCGGTCTCAGCTCTTTGCATCGTGGGCAGAT GAGAGGCCGCTGTGGCTTTTGCTGCTCTTTCGGGTTAT TTCGATGTCTATCGTTGGCTGGTCTTTGTAGT GTTGAAGACACGAAGAGAGTGTTT AATG scaffold 99 TTGGGTGGTGGCTATGGCTGCAGGCACTAAGA T C 100 TTCTCCAATCTGAACGCCACTCTCTCCGATCTCGGGGC 94863:28465 GCAAGCCCACAAACCAAGCTGTTGAAAGAAGC TCAGATTCGAGAGGGAGATAAGTGGTTTGCAACGGCGC ATGCAGCCCGTATAATGCCACAGACTTTGCTG AGCAGGCACGGGGATCAGACCCTG ATTT scaffold 101 GAAAACGAATGCTGCAAATCGATCGGTGAGCC T A 102 ATAACAAATCTTGGAGCTGCATTGTGATGATGATGATG 130551:553 TGTTATGCAACTCTTCCTTGTTTATTTGATGA ATGATGATGATGATTGATAGTCATGGTGTTATGTTTTT TCTTTTTAGTCTCTTTTCATACATTATTGTAA CACAATAATAAAAAAAAGAAAGTC TTGT scaffold 103 AAAGCCTGCTGCGCTTCCCGGGCTCTTGAGGA C A 104 ATAGTTACCATAGATTTTTCTGTCAATACTTTTAAATC 21832:579 GATTCTTCACTTACAATTTGCTTAGCTAATTC GATACCCGGATAGCATTCGCAGCATTCTAAAATCTTTT TTGTAAGAGATCATGCATCCATATTTTGTCAC TCACCCGAATTTCGCTCTCTCCCT CAAC C32090201: 105 GATTATACCCAGAAACCAAAGCAGCCTTAGGA C T 106 CTTAACCAAGCAGCCAGAACAATTTTGGTGTGAACATC 1470 CATTCCAGATTTCGTTTACAACAATCCATAGC AACAGCATGCTGCCTTGCTGACCGGAGACTCCGCCGGA CGAAGTACCCAAAAGCTCATCTTCCCTTCTCT AAAATTTGGGATCCGAGAGTCCCT CAAA scaffold 107 GATTCGAGTCATAACTTGGCACAACTAAACTA C A 108 GAGTAAACACTTTTCCTCTGTTCATCAGACTGACTCTC 117639:1939 CAGTCCTGACAGTCGGATCCACAATCTGTGAA CTGCAGCATTAAATTACTCAATTCTGGATGATGCAAAA AAAAGCAGCAATATCTCGCCCAGATATAAAAA TCAACTTGAAACAGACTAAGTTAT ACCG scaffold 109 AGTCCAGTTACAACAATGTTTGAGCCTCAAAA A G 110 AGCACCAGAAAAGAAGCTTACCCTCTTTGCTCTTAGGC 73281:2531 TAGTATAGAGAAAAGGGACAATAGTAGCAATG TTGCTGTTCTTGAAAAAGCAGCAACTGGCCTTGGAACA CAAATTCTGGCTCTGCAGCCTTAACAAAAACA CTTGGTTTTATCTGGGCAACAGTT GTAA scaffold 111 GTTTTAGATACCAAAAATAAAAGATGTAGATG T C 112 ATCTCTTTTTTGGCTAATGCAGCTATAAAGCATGGGGT 95390:2586 ACCGGAGGAAACAAGCAGCTGGGTCTGCCAAT TCTCTTCTGGGACAACAGTTATCAGAAAGAGACATTAT TCAAAACAGTCTCAGTTGCATAATTACTTGTC TGTGGCGTGCATAGATTACAGGTT TTAA scaffold 113 CTAACTCAATATGTTTCATTCTTGCATGATAA C T 114 TGTTGTAGAAAGAGCAGCAGCGAACATAAGTTTTAAGT 109105:3417 ACAGAACTTGCAGCTGGTGCACTAGCACTCAT TCAAGTAATTTGTTAGTCAAATTTCAAAGTGACACTTC GTTGTCACACCATGTTACTGATGTGCATAATT CTTTATTGGAAAGGAAAAGGTACA GTGT scaffold 115 CCCATGGCTTGGACGAGCTCCGACCTGTGATC T C 116 AGGTGCCATTTCCGTCACTCCCTCACTGAGCAGGAGAA 9670:13701 AGACATCCTCGTTACAAGACTGAGATTTGCAG GTTGATGCTGCCTCATTGATCACCATGGAAGTGAAATT AATGGTTCTGGCTGGCGATCCCTGCCCTTACG ATACCCTTTAGCAGGCAGATTAAG GCCA scaffold 117 GTTGTATTTGCTGCCACGATAAAATTGCTTGG C T 118 GTGGCTCAACCTTTGCTCTATATTCAGTATTTTGGTTA 45478:20587 ACATATCTAAAGTAGACTCTGACTTGCTCCCT CAGCTGCAGGAATGGTAGTCATATCTCTCAACTGTTCT GATTTTGTCTCCCGGCCAACTTTGCTTGCAGA TCCATTGCTGGAGCAGTGAAACTT AACA scaffold 119 TCTTTGTCTTTAATCATATCAAAGACTTCTTG C A 120 AAGACCAATCTTAATTGCAAAAGCATGGACTTCCAGCC 23700:29096 AGCAGCTTCCAATTGCCCACACTTGGAATACA CTTTGTTGAGTGATCTTAGAGATGCACAAGCTGAAGCT TGTCAACAAGTGAATTTCCAACTAAAACATTA GCACTTGCTATAGTAACTGCATTC TCTA scaffold 121 GACATAATGAGTAGACAATGAAGGTATTAAGA A G 122 ACTCTCACATAGTGTTGCAATGATGGATTCGTAGCTGC 10732:30120 TGTGGGCCTATTCAATAACAACGGAAGCAAAA AAGGGAATAGAGATAAAACAAAATTTTTAAAGGAGATT TGAGTACCTTAGCTTCAGGTTCATCTAAGGTG TAATAATAATAATAATAATAATAA TCTA scaffold 123 AATTACAGGAACAAGGGCTAAAGCCAGATCAC T C 124 GAAATTATGAGAAAGGAATTCAATGTAATGCCAGGGCT 16969:31933 ATCACCTTTTTGGGTGTTTTAGCTGCCTGTAC GCAGCACTATGCTTGCTCGGTAAGTCTGTTAGGTCGCG TCATGGAGGTCTTGTTGATGAAGGAAGAAAAT CAGGCTTGCTTGACGAGGCATTGA ATTT scaffold 125 TACCCCATCATTATATTGATTTTGATGATGAG A G 126 TATCGAAAAGCTTGGCTTTAAGTGCTCCTAGTAAGCCC 3884:40695 GTAGTGGAACAGGGAAGAGTATGGCAGCGGCT TCTGAGGCTGCAGAGCTAGTAGGAGCACACACTTGCTC GCGGCAGCCTTGGTGGTGGGCTTGGCATCGCC GAAACAAAAGGGCTCCAAGTTATT ATTG scaffold 127 GGTGGCCTTAATGCCTGGTTCGGGAACAGGCT A G 128 CTGCATCCCACCAACATCCCGGTGGTTGTGGAGATGAT 829:52127 GCAGCAATGACAGCCATAGCCACTTGCTCAAC ACTAGCAGTACTACTAGTCATCGGTGACTGCAGCTACT GCTTTTAGGCCGATTATTAATGAGTCTCCGGT ATATATATATATATATATATATAT GACT scaffold 129 CCATTTTCGCCTTACAGGCTTTACTTGCACAG G A 130 TAATGTCTGATTGTTGAGAAGTTTTTGTACTCGTGAAA 6550:117004 TCAAAGACCGGTCTCAGCTCTTTGCATCGTGG TAGAAGGAGAGGCCGCTGTGGCTTTTGCTGCTCTTTCG GCAGATTTCGATGTCTATCGTTGGCTGGTCTT GGTTATGTTGAAGACACGAAGAGA TGTA scaffold 131 TGTAGGCTGGAGTTTCTGAACATGCAAAAGCA A G 132 GACACTTCTGGTCCTTCACTTAATATTCTCATCAAACT 27604:1398 TTAGGGCCAAAAGGGTCAGATGCCCACAAAGC TATGGCAGTTGAGTCTTTGGTCTTTGCTCCATTCTTTG AGCTGTAATAGGTGACACAATTGGGGATCCCC CTGCTCATGGGGGCTTAATCTTCA TTAA scaffold 133 TCCTCCGTTACTTGGATCAATTCGGTAAGACA G A 134 AGGCAGGCATGGGGCAGCCTAGATGCCCTGATAGGGCG 125644:4761 AAAGTCCACACTAATCTCTGTCCCTTTTTCGG TCTTAGGGCAGCTTTTGAGGAGCATGGGGGAAAACCCG GCACCCGAATCCCCCAGGTCCATGCCCCTGCC AGGCGAACCCTTTCGGGGCTCGGG CGCT scaffold 135 GGGTTCAAGCTCCATCAAGACTTTGGCTGCTC C T 136 CGTTTCCCTTTGCCTTAATTAGCAGCTTCTCGGCTTCA 027:10666 GTCTTCCCAGCTTTTCGTTCTTATGTACCCTG TCTAGTAAGCCTGCACGGCCTAAGAGATCAACCATACA 16 CAACTTCTCAAAAACGAGCTCCACATCATCGT TGAATAATGTTGTCGATCAGGGCA GTCT scaffold 137 GAGAAAATTCTATAGCTCACAGGCTTTAGGGG G A 138 ACACAATGGGCTTGGGCTTTAACCCTTTCACCCAACTC 2502:17437 GTCACCAAAATGCTCACAAGAGAGAAAGAGGA ACTACACCTCGATCTCTTGGAGTCCAGGCCCACTCTCT GCAGCCAAGAGGTACCACTCTCATAGAATGAT CGTTCACAAGCCCAATAGCAGAGA GATG scaffold 139 CCACTCTCATAGAATGATGATGAACACAATGG C G 140 TTCACAAGCCCAATAGCAGAGAAGTAGCGTCCTCTGCT 2502:17515 GCTTGGGCTTTAACCCTTTCACCCAACTCACT GCTATGGTTGCAAGATTTAGTGATGCTGAAACTGGATT ACACCTCGATCTCTTGGAGTCCAGGCCCACTC TGGGTCTGGGTCTGGGCCTGGGCC TCTC scaffold 141 AGCTTGTCTCCCCCACGGCAGCCACTAGCCAG C T 142 TCCTTCCATCCGCCATTTTCAAATTATTTTGATGCTGC 70502:1951 CTGCCACTTGTCCGCCTCTCGTTCAATCCGAG CAAGTGTCCCAATGCATGAAAAAGTACTCAAAATGTCA CTCCAGCAGCCTCCCATGTGCGCCAAGTGTCG ATTTCAAAAATACATTACAATTTT TCTC scaffold 143 CTCACTTTTCGAGGAGATGCTTACCTATCGAA T C 144 CGGGCTTTGATACTACTGGCTCTCTTGAAACTCGTACA 40620:28184 ATGATCATCGATGCAAAAGTAATGGCTTCTAC AGAGAACTAGCTGCGTTCTTTGGCCAAACTTCTCAGGA ACTTACGACGCCTTCATAACTGCTGCTAGAAT AACCACAGGAATACATACTGGTTC TTTT scaffold 145 GAGGAGATGCTTACCTATCGAAATGATCATCG G A 146 TACTACTGGCTCTCTTGAAACTCGTACAAGAGAACTAG 40620:28194 ATGCAAAAGTAATGGCTTCTACACTTACGACG CTGCGTTCTTTGGCCAAACTTCTCAGGAAACCACAGGA CCTTCATAACTGCTGCTAGAATTTTTCCGGGC ATACATACTGGTTCATTTATACAT TTTG scaffold 147 TGCTTACCTATCGAAATGATCATCGATGCAAA A T 148 GGCTCTCTTGAAACTCGTACAAGAGAACTAGCTGCGTT 40620:28201 AGTAATGGCTTCTACACTTACGACGCCTTCAT CTTTGGCCAAACTTCTCAGGAAACCACAGGAATACATA AACTGCTGCTAGAATTTTTCCGGGCTTTGATA CTGGTTCATTTATACATGAAATGT CTAC scaffold 149 CGAGCTCAAGCATTTCATTCTCTCGATTCTCG C G 150 TTCATCCACCGACACCGGCGAGGCAAGCCTCCTCATTC 118158:666 ACGACCCGATTGTCAGTCGAGTTTTTGGGGAA ATTAGGGGCCGCTGCCCACCCATGTTCCTCTGTAATCT GCCGGATTTAGGAGCTGCGATATCAAGCTAGC TACTGATTCGGATCCGGGTCTTCG GATT scaffold 151 CAACGCTCTTCTTGGCCATGGAGACAACTCCC T A 152 AGAGGGTCGGCTGCTGTGAAGCCGAGGCGAGGGAGTGT 41951:881 CTGACCGGAGTCCCACCACCATTGGCGGAGCC GGTGGGGCGGAGACGGAGGGAAGAGGGTGAGAGTTGAA GAAAGAGCGGAGCGTGGAGGCGACGGCGTGGG GGAGAGAAGAACGAGTGCGGGAAG AGAA scaffold 153 CCTTTGGGGAAGCGGCCGAACCATGGCTCGGT T C 154 GGTGCCTGTTGAGGAGGGGTTGATGAGTTACCAGAGCC 95666:9974 TTCCCTGGTCCATTTTCTTTTTCGGGTGGGGA CGATGGAGGGAGGAAAACTCCAGTGCCAGGAACAGGCA AACAGTGTCAGCAGCATGGTTTGTTGTTTCGT AGCGAGGTGGAGGATGCCTCGGTG TGCT scaffold12 155 CATTGACCGCCATGGATCCCCATCAGCTGCTT C T 156 GGCGGTTTCGATGATTACGGAGCGTGGTATGGGAATAT 645:86648 TTGGCAGTATCCCCTTTCGGCTCCGCGAACCA CCAGTACTTGATTAACATTTCGGCGATTGGGGCATTCT AATCCTCTCTCCTCCTCCGTCATCTGACGATG TCTGCGTCTTCATATTCGTCTTCT GAAG scaffold 157 AAGAAGGAAGAGGTTGCCATCCGGGCATGGCG T C 158 CTATCTCTCTTTAGTTCACTGTCGAGTGGAATTTAGTA 6627:26364 AGAAGCGCATTAGCCGGGTTGATTGAAGCCGG GAAGAAAAAGTTGGCCGACGTACAAAGAGAAAAGAAGA ATCAATACTCGTCGCTACTAGCAGCGTCACCA GAAGAGAGTGGAGTCTTATTACAT TCTC C32050599: 159 GAAGAGCTATCTTTAGAAAGTAATGACAAAAT T C 160 AAAAGCATAAAAAATCAACACATTCCAATACATTTTGC 443 CTCTTCAGCAAGTGAATTTAGGTTCACAGCAG AACAATTCAATCAAAACAAACACCAAAAGAAAATTTGT CAGAAAGCCCAAAAAGAACCTGATAATTAAAT TGTTGCAGCAAAAGACACAATGAA GATT scaffold 161 GTCTTACATTTTATATTCTTTTTCAGATATGG A G 162 ATCACCATTCATCCAGGAGTAACACTTGGCCCTCTCTT 20861:14886 TATGCAGCTTCAAAAGCTAGAGCTGAGAAAGC GCAGCCCATTATGAATGACAGTGTCAGTCTCATTATGA TGGTTGGGAATTTGCAAAAGAGAATGGGATTG ATCTAACAAATGGTACACATCATG AATT scaffold 163 AATGGATCCTTTTGCGGCCTCTGCAAGTGAAA T A 164 TGTCACTGGACTCAGCTGAAGCTCGATTACCCTGCTGA 30119:28969 TAACTTTCCCAGCTTTCTTCTTTTTGTTGTTA GAGGAAGCTGCATTCTTTTTAGCTTCTGTCTGATTACT TTATTATTACTTTGGTTCCCGTTTTGCATAGC GGGGGCTGTAACAACTTTTGGTGT TTTC scaffold 165 TGCTGCTTCTTAAGAGTTTTTTAACCCCAATC T C 166 AACAGCTGATCATCAACATTGCAAATCAAGCAAAGGCT 2257:75397 GCCCCGCCCCTGCTCGACAATTAGAAAACCAC GCAACGTCTAAAAGGCCATTGTGCCTAAGCAGTGCCTC ACAAACAACCCTGCAACTCCATTTCACAGCTC AGGTGAAGGTTCGCGGCCTCGGAA CATG scaffold 167 TTAATTTGAATTAGTTATGATTTTTTGAAGTT T C 168 GAGCGCCTGTCTGAACCGCTCATCCGCGCGTGGAAATG 46867:905 TCGGAAAAATCAGAATCGTGCAACAGGGCCAC CTGCAAACTCCTCCCTGCGCCGAGGTTTCTCGGCCAAG GCGCGAGGACAGCACGCATTCAGAAAAGCTGC CACTCCCCTTGCGCACGCGGAAAT TCGA scaffold 169 GGCTCATGCCACTGTTGCTGCCACTTAAACTA A T 170 CGACTAGTGAAATAACTGGTATCTAGTGCACTCTCCGA 65132:21260 TCATCATCGCTAGAATCTTCAAGTTCGCTTGG CGAGGGAACAAATGCAGCCTGCACAAATAATGAGTCGA TGGATAACCATGGTCATCTGAAGTATTCCATG GTTAATGTATAGGAAGCGCAACCA AATA scaffold 171 CTTCAAAACTAGTAATAATAATTATTGGGTGG C T 172 AATGCCACAGACTTTGCTGATTTCTTCTCCAATCTGAA 94863:28441 TGGCTATGGCTGCAGGCACTAAGAGCAAGCCC CGCCACTCTCTCCGATCTCGGGGCTCAGATTCGAGAGG ACAAACCAAGCTGTTGAAAGAAGCATGCAGCC GAGATAAGTGGTTTGCAACGGCGC CGTA scaffold 173 GCATGTATCCAGACCCAAAGCTGGCGAAAACA T C 174 ATTATCCCTATTTCGTAAGGAACAAGGACGCCACATAT 94004:13590 AGACCCTAAATCTGTAGTCTCTGGTTTCACAG ATGTTACAGGAGCGATCGGCTTAGAAACTGGTGCACCA ATCCTAGACTGTTAACAGCATCAGCAGCAGCA ATATGGTGGAGCTGCAACATGGGG GCAG scaffold 175 TCTGTAGTCTCTGGTTTCACAGATCCTAGACT T A 176 TACAGGAGCGATCGGCTTAGAAACTGGTGCACCAATAT 94004:13632 GTTAACAGCATCAGCAGCAGCAGCAGTATTAT GGTGGAGCTGCAACATGGGGATTAGTCAGACATAGCCA CCCTATTTCGTAAGGAACAAGGACGCCACATA ATTCCTTAATCCACCTCAATGAAA TATG scaffold 177 TTTTTGATGTTAAGAATTGTACGTTGAGACAT T C 178 TGCTTCTTGCTGCCAGTTTCTCAAAGAGGCTCATAATG 39420:9067 GAGAACTAGCAGCGAGTGTTTCTCACCTGCAT TTATGATAAGCTTTTGCAAACATAGAGAAAAATAGGAT CATAGTTTTTGAGAAAGTCAGGAGACAAATTA GAAACAGAGAGTTGTATTAATAAT TGGT scaffold 179 TGAGTTTTGCAGGCGCAGCTCGGCCTGATGCA C T 180 GACTGCAATTCAGGTGGCTGCAGCCAACCCGAGTCTGT 42291:6484 CCAGAGAACATAAGGTCCATTCTCATCAATCA TATCGAGCTTTTCATGGAGTCTGAATTCTGTTTGCAGC GTGCACCTCAGTAGATGATCAAGACTGTCAAT CACCAGGAGATAGCCCAACTAGAA TTCT scaffold 181 GAACTTGATCAATCCCATAACTCAGTCCTCCA G T 182 GACATGTTCTTCCGCTGAATGAGGCACCCATAACTCTT 23828:34435 TTGTCATGGAGCCAGCGGCTCTTCTCCCTACC GCAAGTATAAGGATCCCAAATGATGCTGCTGTCCGGCG CTGCAAATCAAAAGAGTCTTGGCTGCCATAAA GGATTGACCAGAGGCTGTCTGGAA ACCC scaffold 183 TGCCTAATTTGTTGTTTATTTGTCATTGGTGG C T 184 GCTCAGGCTGAGAGACACATCCCCGCATCAACACCCAT 15017:4539 CAGCATGATGCTGCATGCCGTGTGATTGCAAG TACAGTAAATGCGTCTGCAGTTAGCAATGGAAGAACAG ACTAAAGAAAGAAAGAGATGAAGCAAGATCAC GTCCTTTTTGTTTTATATATGCTG TACT scaffold 185 GGCCGTTCTTGGGGACGACCTCTCCGTCCGAT T C 186 CCAATACAAAATTGGAGAGCCTTGGTGATGAAGATGAA 16607:2589 TCGCCAAACTCAGAGCCTCCTTGTCTCAGTCG GAGGAGGATGAAGATGATGAGGTTGAGAAGTTGATTAG CCTGCTGCTTCCATTTCCGGCACTGGTGGCGT GTGGGCCAAGGACGCTGCTCGCCT TCGT scaffold 187 TACATACATACATACACAAATAAATAATTATA G A 188 GCGTCTCTGGCACCTGCAACCATTGCAGCTTCGGTCCA 27758:4907 AATAGTAATACCTCCACTAGAGCAGCCTCTTT CCCCAACTTAAGCTGCACCAACTCATCCCAAACGCTAC CCTGGGAAGTGACCCAATTATGGCGGGAGACA AATTAAAAATTCACCCCCAATTTT CACC scaffold 189 TTTTAGGTGTTTTGAAACAGTCTCAGAATCAG G C 190 AGTAATGGAAAGTTGGTTTCTATCGATGTCTTCGAGTT 20809:7695 CATACGAATTTTGTCTTGCTGAACACTGATGC TGTTTCTGCTGCTAAGAATTACTGGTCTTCAGAAGTTC TGCTTGGGCAAGAAATGTAGAGAAAAGATCCG TCTCTGTTGGTTTTATGGTTCTAC TTTG scaffold 191 TATTCCCTTCTTGGGTGCAAATGTGACATTAG T C 192 TACCACCTGTGTGCTGCAAATTCTTAAACCTGTCATTC 36583:13571 AATCTTTACCAATTGTGTTAGCATGCTGCCCT CTCTTTCTATTGATGACTGTAGTCATTAAAAAAAATTA TTCTCTATGGGTTACGAATCGCTTCTGAGATA TTAACTTAAACTAAAGTTAGGTTG TCTT scaffold 193 TCACTCTCTTCCTAATGGGATTGACCATTAGT T C 194 TATGCCTTTGATCGAGCTTTCGAGGGCTCGGTCTCTTC 36500:1728 TGGAATGGTTCTGCTGCAAATGGTCCCATGTT CTTCGCAGCTCCCTTGGTTGGAATTCTGTCGGAGAAAA TGCTGAGGTTGTCCCAGCCAAGCACCGGACCA TGTTCGGGTATGATTCGAAAGGGG TGAT scaffold 195 TAATGGGATTGACCATTAGTTGGAATGGTTCT C T 196 CGAGCTTTCGAGGGCTCGGTCTCTTCCTTCGCAGCTCC 36500:1740 GCTGCAAATGGTCCCATGTTTGCTGAGGTTGT CTTGGTTGGAATTCTGTCGGAGAAAATGTTCGGGTATG CCCAGCCAAGCACCGGACCATGATCTATGCCT ATTCGAAAGGGGTGGATCCATTGT TTGA scaffold 197 TGACCATTAGTTGGAATGGTTCTGCTGCAAAT T C 198 GAGGGCTCGGTCTCTTCCTTCGCAGCTCCCTTGGTTGG 36500:1749 GGTCCCATGTTTGCTGAGGTTGTCCCAGCCAA AATTCTGTCGGAGAAAATGTTCGGGTATGATTCGAAAG GCACCGGACCATGATCTATGCCTTTGATCGAG GGGTGGATCCATTGTTGGGGTCTA CTTT scaffold 199 CAGAGAAAGAAGAGAAAGGTACTAAAATTGGC A T 200 GGGACACGTGTCAAGCATCACTCGGTTGAGAGTGGGGC 153198:2269 ACAGACTAACCGGGCCTCCATGGTGTTGAGTG CCATCACAGGGTGGACTCGAGGTGGGCCTTTTGCCTGT GGCCCCCACCCACGAACTGTAACGGGGCCCAT TTCATGCTGCGTCAGGTAAAACCA TCAT

TABLE 7 Upstream, Allele and Downstream sequences for SNPs from Table 5 SEQ SEQ SNP Name ID Upstream Sequence Minor Major ID Downstream Sequence scaffold 201 TCCAGTAGCCAAGGTCATCGGCGGTGCCCTAAACAAG C A 202 CGAATGCATAAGGCTGCTGTAAAGAATGTTTACGAG 13038:51303 CTCTCCAAGATTAAGGTTGTGAGGCTTTTAAGTTTGG AACAAGAGGTTCATTCCACTCGATCTCCATAGGAAG ATTGCTCGTGTGTTGACGGTGATATC AAGATCAGGGAGATTTGCAGAAGGCTTA scaffold 203 TCTTATTCAACCAAATGCCATAACCGGCCATAGCTGC A G 204 TGAACACTCGGCCAAAGCTTGCTGCCTAGCCCCTTC 25092:11841 ATAAAAAATATCAGCTATAAACCTCCTGGGCTTTCTG CCAATGAGATGCATAACTGGCCAAGAGTAAGGACAA CTATTCATCCAATGTATCCAGTCCTC GAGAAAAATAAATCAGAATGGCTCCAAA scaffold 205 ATGACCGCTGTTCCAATGCTGCCAACTTGGTGACTGA C T 206 AAGGAAGACAAAGAGAGCGAGCTACAATCTCTGGCA 23837:26190 AACAAAGTTTACTTCATGTTACTAGTGTTCCTCTGCC GCAGCAGCCTTGGAGAAGGACTACAAACGAAGAGCA ATTGGGCAGCTCGCAAAAGGTCGGAA CCTGCAACACTGTCCTTGATTACGACCG scaffold 207 TAGTAGTGGTAGTGCCACTCTCGGTGGTTTAGCCAAA C A 208 AAACCGCTACCGATAAGAGTGTCATAGCGGCCTTGA 152474:1505 ATCGCCCTCCAAGCAGCGGCTTCAAGTGCCAAAAACA AGGATTGCAGTGATAATTATGATAGCGCCAATGAGG CCCAAGCCCAGATCACTAGCCTACTC AACTCGGTGACTCGCTCAAAGCTATTGA scaffold 209 TGTACAAAGATCTTTGTGAGAAGACACTGCGAGCAGA G A 210 AGTGCCAAAAACACCCAAGCCCAGATCACTAGCCTA 152474:1465 CCCTAGTAGTGGTAGTGCCACTCTCGGTGGTTTAGCC CTCAAAACCGCTACCGATAAGAGTGTCATAGCGGCC AAAATCGCCCTCCAAGCAGCGGCTTC TTGAAGGATTGCAGTGATAATTATGATA scaffold 211 TCCAATTTCAGTGAGAGAGAGAGCTGCTGTATGGAAG C T 212 TGAACAAGCTTAGGGATCTCAAGGCTGAGCTCCTTT 13038:51162 CTAAAAAAAAGCAGCAATGACAAGAATCAAGGTTGAC TCCTTCCAGTAGCCAAGGTCATCGGCGGTGCCCTAA CAGCTGAGGCAGAAGAACAAGACCTT ACAAGCTCTCCAAGATTAAGGTTGTGAG scaffold 213 ACTGCTGGAAATGGTAGTGTTCTTTTCACTATTTCTT A T 214 TCCCTAAATCTAACAAACCAACTTTTGCACAGTTTT 5841:136325 AAGTTGCCTCCCAGAGAGGTAGTTTCATCAATGTGCA CTGCTGACAAAGTAGCATCTTTTTGGACACTATTAT AGCTGCTGTCTTCATCCATGGTGGTC CATGCAATGCAGCGACCTCAATACTACA scaffold 215 CTGTAATAGCTGCTGCTGCTGCTGAAGCTGTTACTCT A T 216 CAAAGTACTTCTGTAGTTACTTTAGAAGCTAGTTAT 5876:22669 TGCAAAAGCAGCTGTGAGGGTTGCAAAGGATGCTGCT TCGGATTTTAAGGGTGTTCATAATATGAAAACTACA CTGCTAGTGAAAACTTCTGAAAAACA CAAGCTGCTGTATTAGGAGATTCTGTGG scaffold 217 TTCTTGGTTGGTGTATATTGCAGCACTTTCACCCTTG C A 218 AAGCAGCCCAATCTTGTACTCACTTTGATTTTGTTA 764:75880 AAGATTAGGCTAGGGGGCACTTTACAAGACAAAGTCA AAAATGGCTCTGAATTATTTAGCTTCTCTCATGGTT TATACCAGAACGAGAGTGAAAAAACT GCTTATCTATGTCTCGGTGGGATCAACT scaffold 219 CATATACATGCTGACTGGGCAGCATGTGTAGGACACA C A 220 AACAACACGCAATACCGAGGTCCTCAGCTGAAGCTG 32076:9119 AGAAGGTCCAAAACAGGTTTTTGTGTTTTCCTTGGGA ATTGTAGGGCTATGTGAAACACTAGTGAATTGGTAT GATCTTTAGTGTCCTGGAAAAGTAAG GGCTGCTATCATTACTAAAGGAACTGAA scaffold 221 GAGGTAGACTTTGTATTTTGAAGCTTTTGGATATTAG T A 222 AGCAAGTCATTGAGGGTTAGCTTAGAGAAATCAAAG 7992:917 AGCTATCAGGGTTTTAATGGCTTCCCAGGTGAATAAC TCCCTAGGGTTAGCTCTACAGAAGACAGGACCTAGA GATGGCGTTGAGAAATTGTTAGCTGC TTGGAAGAGATTAACCAACGATTACCTG scaffold 223 ACACTTTCATTAAATATATGTCCGGTATGTACAGAAC C T 224 TGCATCTTTAGACAAATTACACATTGAAGTTGATAC 118405:2916 GCAACATTCATGGCATAATTAACACGTCAGCCAAATA TTCTAGCTGAGCTAGGCTAGGCCGACTCGCAGCTAA ACATTCAATCATAATCAATTGCAGCA TATTTAATCAAATAAAAAGTACCTAAAA scaffold 225 AGGTGAGATATGAGAAGGGTCGAATGGTAAAATATAC G T 226 GATTGAAGGAGGAGCGGACAAGTGTCGCTCATGTGA 2418:77480 AATGTGCAATTTATTGGCTAAGAGAAATAGTAAAAAG TGGCTGGAGGAGAGGAGCTGCTGGAGAGAGAGGGGA AGCACATGTATTTGCTGCTGAAACTC CAGGCGGGTCCCACGCAGCTGGCGCTGG scaffold 227 GTTGATACTTGACTAATTTCATATGGTGCTGTGGAAA T C 228 TGGTTTTATAAACAGTTTGCCGATGGCTAGTACGCT 34829:1873 TGTAACAGGTGGATGTTGTGGATACAGTTGGTTGCGG GTCAATTGCAAACGCAGTTGGTGCTGCAACTGCTAT GGATAGTTTTGTAGCTGCTATTGCAT GGGTTGTGGTGCTGGTAGGAATGTGGCA scaffold 229 TATAGGTGTGTTCGGCTATGGAGATAAGTGGATTCTT G T 230 AGATGGCACGTGCTTGTCACATGCGCATCAGCAGCT 38125:4641 CTTGTGCTTAGTTGGGGCAGCGAGAATAACGCACAGA GGTGGGCCGGACCCATCCAAAGCCCATTTTCTAGAA GCTCAAAGGATAGTGTCGATAGCAAC GCCAATTGCAAGGATGATCAGCAGAGGT scaffold 231 TTCTTACTCCGATGTGCTGTGCAGATCACTGGTCAGT G A 232 TTTTTGCTGCTTGTCTTGATATTCTTTCATTGTGTA 37469:74270 CAGCATTATCATTCAAGGGAAGCCCCTACTGGATGGC TGATCTTGATTCTATTTCATCCTTCTTCCTGCCTTT ACCTGAGGTAAAAATCTTATGAAGTT CTCCCAGGTAATAAAGAATTCAACTGGC C32100775: 233 ATTTGAGATCCTTAGCCGATAGAATTTGTTGGTTAAG T C 234 GCCATGGACGCTCCAATTCTTTGTTCCTCTGCTTCC 1618 TCTCTGAATCTCCTCATCAGCTTGTTTTAGTTCCTTA AAATGTGCAGCATGTGCAGACTCCAACGACTCCTTC TCCCAATTAAGAGAATCTTGCTCCCT GTTGCAATCAGCTCGATAGTGAGTTCCT scaffold 235 TTGGTTCTTCTATTGGGTTTACTATACTTTGGAACAT C G 236 ATGACACTGCTTCCAAAGCAGAGAGTTCCAAAGGTT 5190:41424 GAATAGGCGAGGGTGGATTGAGTATTCTGTGGCTGCC TGGGGAGTTCCCATGGTTCCATGGCTGCCATCTCTG TTGATTTGGTCCGTGGGGAATTTGGG TCTATTGTGGTTAATCTTTTTCTTATTG scaffold 237 GGAACATGAATAGGCGAGGGTGGATTGAGTATTCTGT G A 238 AAGGTTTGGGGAGTTCCCATGGTTCCATGGCTGCCA 5190:41454 GGCTGCCTTGATTTGGTCCGTGGGGAATTTGGGGATG TCTCTGTCTATTGTGGTTAATCTTTTTCTTATTGGG ACACTGCTTCCAAAGCAGAGAGTTCC TCTTTGGGAATGGTGGCCTTCTTCAGGT scaffold 239 GTATTGGACCTCGATCTCTCAACTTTCGACCGGCTTC A G 240 GCGCGTGAGAGGAAGCGTTGTTTGCACGGCGAGCGT 49917:1105 TGGAGGTGAACGCCCGAGGAGTTGCGGCGTGCGTGAA GGCTGCCTCTGTCGGTTTGAGGACACGGACAGATTA GCATGCGGCGCGTGCGATGGTGGAGC CTGCATGTCGAAACACGCGGTGTTGGGG scaffold 241 GTCACCAAATAAATATTGTTTTTTAATATTTCAGAGG T A 242 CTGCATATCATTTTACATTTTCATGTTTCTTTCTGC 4775:75747 AGGTTTTGCAGGGAGTTGCTGCTGGCATCGATCTTTT TGCTAACTTGGCCAAACTCCGATGATGTAAATGACT CGACTCTGAGTATGTTTGTCCTTTCT GTTTTGCAGGTATATTTACCATCTTACA scaffold 243 AAACTTTGGCTGCACCTCCTGCTGAAGAGAGTGTGCA G A 244 TGCATTGTTGGCCGATCAGTTGGTTGTTTCTTGCTG 26152:15432 TTGCGCTGTTGCTGTAGAAGCCAGTTTAGTTGGCAAG CAAAGCAATGCAAGTTGAAATACCTTCCTAACCGCC AGACTGCTGAGAACTCGTGTTACTTC CCGAGATCCTTACATGTAGCTGTGATTT scaffold 245 CACAAACGTTTTTATCAGCTCTCCATCTTCGCTACAA G A 246 GGGAGTGCTGAGAATCAATGTTTCTTAGAGCATCAG 5841:135056 GTTTCATTAGATATTTGACAGCCAGACATGGCATCTA GCACCAACTCCATAGCTTCATCACTGGAGGTAGCAG ATATGCATGCATTGGATGCAGTAATC CGGACACTCCATTTTGATCAACAGGCAA scaffold 247 CCTTAGCATCTCCTGATTTTTATGATGTGAGTCTTGT A G 248 GGATGTGATGGCGACCTCCGGACCAGTTGCCCTAAC 5876:106401 TGACGGTTTCAACTTGCCCATAGTCGTCACACCACTC GAGCTGGCGGTCAAGAGCAATGGGAAAACGATTGCC CACGGGCAAGGAAATTGCAGCGTGGC TGCCGGAGCGCGTGTGACGTGTTCGATA scaffold 249 CAAGAACTTGCCTTGCTGCTGCATCTGCTGAACTGCA A G 250 ATCAAAACTTCCATGCCACGTGCAGCAAACAGTCTC 5113:138895 GACAACATTCATTGCTCCAATCCTTTCTGAATAAAGA ACCGATGATGCATCAGCATCAAGGCTTCCACTAGCA CCCAAATTTTTACTGTAAGACTGAGC AATCCCTTTAAAGAAAAATAAAATAATA scaffold 251 TATACAACAGAGACTTCACTGCCAAACTTAATCTCTC G A 252 TCATCATCATCATACAACCAGAGAAAAAAAAAAACA 5113:239777 TGTTTAAGCAGCACCACCAGTCCACCACCAAACACAT GTGATGCATTTTACAGAGAAAGAAAAAAGCTGCAAT TTGAGCAAACACTACTAGTTCTCATC GATTTCTAAGCAGCCTTTTTTTAAACAA scaffold 253 TTATCAGCTCTCCATCTTCGCTACAAGTTTCATTAGA G A 254 GAATCAATGTTTCTTAGAGCATCAGGCACCAACTCC 5841:135067 TATTTGACAGCCAGACATGGCATCTAATATGCATGCA ATAGCTTCATCACTGGAGGTAGCAGCGGACACTCCA TTGGATGCAGTAATCAGGGAGTGCTG TTTTGATCAACAGGCAAAGAGAGATCAT scaffold 255 ATACTTCATATTCCATTTCTCTATCTCCACTCTGCCT A G 256 GTTAAATCTTCCACCTTCCGCTGCAAAAGAGGAACA 25099:7321 CTGGCATGAAGTAGTCCTTCAGGTGGTTTTTGCAGCA TTTATAAATCAATGTACAATATCAGAACTAGGGGTG GAAAGATCTACGGCCTGAAAACTCGC TGCATAAATCGATTAAATCCATTAACAA scaffold 257 GCTAATGGCTCTTATTGGTCAGTCGTTGAAGTGGCAG A C 258 TCTTTAAAGTAACAATTTGTTCTCCCATTCCAGGGT 14172:40875 CAACACCAAGGTATATATACAATCTTATTGTGCATTG TACTTCCTCCAGGCACACAATTTGACTTATTTAGAG ACAAGAGAACCATATTATCTTGCAAT GAACAGCTGCTATGAAACAAGATGTAGA scaffold 259 AAAGGGCATTCAATCCTTACGGTTCAGCTGCTTACAA A G 260 AAACCCCTTCACGTTTACGGAAGCCCAACTTACGAG 158332:502 CTTCATCACCATGGGAACTTACAGAGGAGGACTTAAC TGTCAATGGCTGCAGAATTCTTCTCCCTCCTCCGTT ACCTTCGCCATTGTTGCAATAGCTTC ATCTCAACTGTTGGGTACAAGATCCTTC scaffold 261 CTACAAAGGTTGCGTTTGGACCGAGCTCCTTAGCCGT T G 262 GTGGCTGTTGCTTTGCCTATTCCGCTTGCTGCTCCT 16869:149709 GGCTAGGCCGAGATTGTGTTGGATGTCTGCTATGACT GTTATTAGTGCCACCTTCCCATCAAGCCTGTTATTT ACTTTGGCACCATTGTTGATGAATTT TCAATGAGTGAAGAAATTGTCTGAGTAG scaffold 263 AATTGGCAGAGGAGAGTTCATATGCCAAAGGTTTAGC C T 264 GAGAGACTAGCAGCTGATCTAGCCGCATCCAAGAAC 114539:1119 TTCAGCTGCTGCTGTTGAACTGAAGGCATTATCTGAA TCCCCCACTCAGCGCAAAAGTGGCAGTATGGTCAAG GAAGTTGCCAAACTGATGAACCATAA AATGGGCGAAGAGAGAGCATGAACAAGC scaffold 265 TTCACCCAAGAAAGAAAAATGTGATTGTCACATATGT T G 266 TTATTGTTATGAAATCTATGGTTGTTCAGTCTAGTG 3842:272682 TTGCTGCATGTGCATGGACCATTGGGTTTAATCTTGC CATTTCACCACAAAAAAAATGTGATTGTCGTATATG ATCATGCTGTTTCTATATTATGATCT CGTGCTGCATGCATGGGCCATTGGGTTT scaffold 267 CACCAGCCCGCCTCATGTCATGAAAGGTTTGAATAGC G C 268 ATGCTCAATGGAGTTGCAAAGAATATATCCCTTGCT 60331:8510 AGCAAAGCCATCATTGTTATGAGAGCAACAAGTGATC AACTTAAGACTCCCAGCAGCAGAGTAGGCAGCAATC ATGGCATTGTAGAAAACAGTATCTCT ATTGTCGTTCTCGAAACAATATCTGGTT scaffold 269 TTCACGGAATTTTAAATATTTTTACGATTTTTTTGAT G A 270 GGAGAGAGTTAGAGCAAAGACGATGGTATGGAAGAA 2360:22109 TTAAAATGAAATACCTTCAAATCCTCCGACTGGTGTA GTGGCTAAGTGCTCTGCTGCAGTAGTACAAGTAGTA AATAGCTGCAATGGTTGGACAGAGAG TATATATGGAAGGGTATAATGGGAAATC scaffold 271 GCAATTTAAACAACCTCTCCTTCACTGAACTCACAGA G A 272 TCGGCATAGTACACTGGCGGTACCAAGGAGACAGGT 72613:1728 AGACGATGACAAAGATCTCTCCATCTCTGCCTCATGA TTGGTGCAGCGAGCCATGGTAAAACACATGCTATAT TACAGTCTCCCTCTATAGGCAGCAAG ATGAGCTTCTGCAATTGGTCAGAAGTAA C32052717: 273 TGGTCATGACGTTGTACTCAACTGAATGTGCGCTGCA A T 274 CGGTCAAACATGATGACACGGTCGTTGTTGAGAAGC 309 GTCTTTGGCCCCAGCAGGGCATTTCCCAGGCGCCAAT TGCATGTGCATGGCCGAAATGCCAATGCTTGGTGTC GATATGTTAGAGGTGCCGAAGTCAGT AAGAATTTCCACCGGCCACCGGCTGCAT scaffold 275 TTTCGCCCAAAAATTTGATGCTACCGAAACCGTGTCG C T 276 TCTTGGATTCGTGGCTCGGTGTAGTAATCAGAGCGC 71943:13435 TCCAACAACAAAGTCCTTGACACGGCAGCAGAATCCT CTGAGCTTTGGCATTTGAGCCTCAATATCTGCACCG GGTTCGGCCCTTTCCTTGGCAGCAAG TGCTCGTACACAATAGCAGCCTCACCAG scaffold 277 GTCCAACAACAAAGTCCTTGACACGGCAGCAGAATCC T C 278 CTGAGCTTTGGCATTTGAGCCTCAATATCTGCACCG 71943:13471 TGGTTCGGCCCTTTCCTTGGCAGCAAGTTCTTGGATT TGCTCGTACACAATAGCAGCCTCACCAGCTCTGTGC CGTGGCTCGGTGTAGTAATCAGAGCG CCGCTAAGGGTCTTATAAGAATCCCCCT scaffold 279 CCTGTTGTTCCCGAACCTTGGAAGCCACTACATACAC G T 280 GTAAGGGATGTTCATGGGCATGTGACTACTGCTTAC 128544:170 TGCCGCCTCTTCTTTCAGGTCTTGAAATGAATGTTGA TCGAAGGCACATTCAAATCACATGAGATGAAGTTAT TGCAGCAATCAGTATTTCTACTCGAT GACACTTTTTCATAGCCTTCTTTGGGCA scaffold 281 TAAGAGTGAGAATTTTATTATGAAGATTGAGGCGATT T C 282 TGAGTTTGCTGTTGCTGCTGTTGTTGTTGGGAGCGT 98263:1069 ACCAGTGAGTACAGAAACGTGTTCTGGGAGTTTAGGG CGAAGAGAGGAGAGAGGTGGTTCGATACGGAGGCGG GCATTGGGGTTTTGGGTTTTTTGTGG CGCTTCCTGCGACGGCGCTCAGCTGCAG C32058675: 283 TTTTTGTATGATTAATTTATTATAATATACAGATAAT A G 284 AATGGGCCTAGGACTGGGCCTAGAATATCAGCAGCT 292 AACGAATGGGAGATTCAAGAGCGTGGAGCATAGAGTG TGCTTTTTTTATCCAAGCATTCCCAATATTGCGAAA TTGGCAGCTGGGGGAGGTGGGCCTGA CCTTACGGCCCAATTAAAGAGCTTCTCT scaffold 285 ACCTGAAGATGCCTAATTAAAGGCATTCCATTCTTCT C T 286 GAGCTCTTCTATTTCATCTGATGTCAACAGGTCCCG 823:11824 TCCTTTTCAGCTGCCAATGCTCGTAAATGACTTTAAT CTGTTGAGAATATGCAGCCTTCTCAAACATGTCCAT TACATCCATGGGCCCAACTCCAGCAG AATTTTCTCAAACATCTCTTCAGATATC scaffold 287 GGTTGGGGCTACAATAGCTATGGTCAGGCAGCCAATG G T 288 TAGCTTTATCCTTAACACTGCTTTTTCGTTTTCTAT 75287:5899 AGAAATCTACCTATGCTTGGTTTCCATCACCAGTTGA GTTCATGGAGCTCCCTTTGCAGGTGCGTTGGCGAGG TTGGTATGGCAAAATTATATCGTTCA TGCGAAAACTGGCAGCTGGTGGTGGCCA scaffold 289 CGAGCTCCTTAGCCGTGGCTAGGCCGAGATTGTGTTG C T 290 CCGCTTGCTGCTCCTGTTATTAGTGCCACCTTCCCA 16869:149730 GATGTCTGCTATGACTACTTTGGCACCATTGTTGATG TCAAGCCTGTTATTTTCAATGAGTGAAGAAATTGTC AATTTGGTGGCTGTTGCTTTGCCTAT TGAGTAGAAAGAAGGTAAAGAAAGCAAT scaffold 291 TTATTCATGTGGAAGTAGCTCTATAAAACTGTCTCTA C T 292 ACATATCTGTTGTACCTCTTTCCTGGAACAGCTTCA 3842:543149 ACATGGTATTTAAAGTGTTTGCATTGGAAAAATGTTC TGTAGCTGAACTAAAACCCACAGAGTATAAAGCTGC TTACCAAATGCAGCTTGAGCCAGTTC CAACAGTAGGCTATGGTCAAAGAAAGTA C32058613: 293 TTGACATTACTAACAATTACTGAAGCCCCCATTACAC T C 294 AGAAGCAAGCACCTATTTTTTGCTCTTCGAACTCTT 508 TAATTTGGGGCCAATAAGCTTGACTCCTCGCTTTCCA CCTCTTCCTTATCCATTTTATAAGCTGCTAAATCAT AACGTGTTATATTGTTGCTGCCATAA GAACACTTAAGTCTTCTAGTTCAGCCAA C32058613: 295 CTTGACTCCTCGCTTTCCAAACGTGTTATATTGTTGC C T 296 ATAAGCTGCTAAATCATGAACACTTAAGTCTTCTAG 563 TGCCATAACAGAAGCAAGCACCTATTTTTTGCTCTTC TTCAGCCAAATTTTGAGCACTTCTATACGTATTCTG GAACTCTTCCTCTTCCTTATCCATTT TTGCTAGGACAGAAAAAGAAAAGGTGTT scaffold 297 CGGTGGTGGCTGTGGTTGGGGTATGCACGTTGTCGTT C T 298 TGGGCTTATTTCGACCGTGACTTCTCTCGCTGGATC 7146:70340 TAAGAAAATAGTGGGAACATACTTGGTGGGAGTAGTG CACCCAGTTACCGCTGATGAAAGGGCCTCTCATGCT GGCCTTGCCGGGGTGTTTTGCCCAGA GCTTCTCACAGATCTGGACTACCAAGGC scaffold 299 TGCAATCCTGTGGTGCACTAGAAACCGCCGCCGCATC G A 300 CCGTGTGGCTTCTCGTTCTGTTCTCGCAAGATTTGC 23125:41276 AGCATCTGTCTCCTTCCCACTGAAAAGCTCCAGTTGC AGCCTTACAGTTTGGGAGCTCAGATTAGTAGATGGG AAACTAGACAAAGCCTCTTGCGTAAG GAACGGTCAGTTGATAAACTTGTAGAGT scaffold 301 AAAATATACAATGTGCAATTTATTGGCTAAGAGAAAT A C 302 TCATGTGATGGCTGGAGGAGAGGAGCTGCTGGAGAG 2418:77508 AGTAAAAAGAGCACATGTATTTGCTGCTGAAACTCTG AGAGGGGACAGGCGGGTCCCACGCAGCTGGCGCTGG ATTGAAGGAGGAGCGGACAAGTGTCG CAGGCTGGGCAGGAGGAGACAGGCGCTT scaffold 303 CCAGCTCTGCCGGATTCCAATCCGTACCGACCTCGCC T G 304 CCGGCGAGTCATCTTCAACGGCAGCAGATTCTGATT 12000:86305 TTGGCGGAGCCTCTCTCCGTAACCGGAACCCTCCGCT TCGATGCGAAAGTGTTCCGTAAGAACTTGGTCCGAA GCCGGAAACCTTTCGTCATCCGATGC GCAAGAACTACAATCGGAAAGGTTTTGG scaffold 305 GTTGCTTTATTTGAATTTTTGAGCTTCATGATCTGGC T G 306 GGGGTCTGTTCTGCACACAATAAAAGAACATTTTTA 24181:60784 AATGGAGTTAATACTACACAGCTCACTAATAAACGAC GGTATATACCAAGATAGGCTGCTCTGGACATCATTT AAAAGTTTGTTGTCGTTTTTTGTTTC AGCAAGGGTCACCATCTTCTAGCAAAAC scaffold 307 ACAGTACCAGTACATCAGGAAAGAGCAAGAGCAAGAG G C 308 ACAATCCTGCTCCCCAACACTCTCCAGACCACCCAA 26621:72993 CAAGAGCAACGACGCCTACTACCAATAACCCAAATAG CACATCCAATACTACTACTACTACTACTACTACTAC GGCAGCAAGGATGATGATGATGACCA TGCTGCCTTCTTCAGGGGTAGCACCATG scaffold 309 ACGCCACTGTGTTGACGTAATTTCTACATGTAGCAGC T C 310 GCCGACGCTACTGTGTTGACGTGACTTCTACATGTA 6391:16360 GTAATGACAGTATTCTATTGCTGGAACGCTATTTGCT GCATTGTAATGCCAGTATTCTATTGCTGCAATGTTA GAAATGTTATTTCTTCATTTTTGTGT TTTCTTCATTTTTATGTCGCCAATGCTA scaffold 311 GAAACCTCTGTGCCTTGGAATTCTTGCTCTTAATTAG A T 312 ATTGCACAAGGTGTGTAAGAACCAAAAGCACTCTCT 88759:12655 CCATATTCGATACACACCTAGGCCCAAAAGAACCAAA ACTATCTTTCCCCAAACCCCATAAGCTGCAGGCTTA TGAGAAGTAGAAATGACTAAAGACTC CAATACCAACTTAGTAGCTCAAACCTCA scaffold 313 TGGATGGCACCTGAGGTAAAAATCTTATGAAGTTATT C T 314 GCCTTTCTCCCAGGTAATAAAGAATTCAACTGGCTG 37469:74336 TTTGCTGCTTGTCTTGATATTCTTTCATTGTGTATGA CAACCTTGCTGTGGATATTTGGAGCCTTGGATGCAC TCTTGATTCTATTTCATCCTTCTTCC TGTTTTGGAAATGGCTACTACAAAACCA scaffold 315 TCTGCCGGATTCCAATCCGTACCGACCTCGCCTTGGC T C 316 GAGTCATCTTCAACGGCAGCAGATTCTGATTTCGAT 12000:86310 GGAGCCTCTCTCCGTAACCGGAACCCTCCGCTGCCGG GCGAAAGTGTTCCGTAAGAACTTGGTCCGAAGCAAG AAACCTTTCGTCATCCGATGCGCCGG AACTACAATCGGAAAGGTTTTGGCCATA scaffold 317 GCTTGACACAATCATAAATCCAATCAGAGGTAATTGT G A 318 GTGACCTTATTTGTCAATCTCTCTACTAATTTGGTT 6143:103796 ATGTATCCCCCATTTACAAGCAGCCTCATACTTTGGT CCAAGAACAAAGCATAAATTTCTCAAAAGCAGCCGA CCACTTGCAAACTTGCAAATGAGATG TCTTTCTCTTCATATTGTGAAACACAAA scaffold 319 GGACTCAATCACCAATGCTGACCCCAAAGCTGCATTC A G 320 ATGCCATATTTGTTTTCGCTACAAAATGTGGCATTG 33135:78155 ATTAACTCAAAGTAAGAAATCTAGTCCTCTTCCAATG CGAGCTAGCTGCTGGGAAATTAGAATTGGATCACAA CTTAATTGGCCAACCCGAGCTCTCGC ACACAGCAAATTTATTTGAAATCCCTAC C32058675: 321 TATACAGATAATAACGAATGGGAGATTCAAGAGCGTG G A 322 TATCAGCAGCTTGCTTTTTTTATCCAAGCATTCCCA 317 GAGCATAGAGTGTTGGCAGCTGGGGGAGGTGGGCCTG ATATTGCGAAACCTTACGGCCCAATTAAAGAGCTTC AGAATGGGCCTAGGACTGGGCCTAGA TCTCTCACACCAACCCACCACTCTACAA scaffold 323 TTTCCAACCATCCTTGGATGGCTTCCCTTTCATAAGT G A 324 TGTGAGCCAAGTTAAAGAACAAGTTTGAACCTTACA 1976:5193 GAATCCATCAGCAGCCACCTGAGGGTCATGCATTATT CCCAAATTTCGGGAAAGCTTGAGCTTGTTTAGAGTT TCCTGAAAGTAAACCAGAACATTAGG GGGGTTTGATTGAAAGACATGAGAAGCA C32098343: 325 AAAGCTTCAGACAGTTTAGAGGCAAGCTGTTCCAGAG T G 326 CCGCCATACATCAACATTATTCTCACAAACCATGCA 2061 GCCTCAAGCCTACAGCTATCACTCTTTTGTACGTTTC GAGATCAAGGTATGCAAGATACTGAAGAAGAGACCT ACCACTTTCCTCGAAAAAGGCAGCCC CGGGCTGCTCTCTTCTAGTGCTGCAAGG scaffold 327 AAATTCTAAACCATGATAAAGAAAAAAGGTTAGAGGA A G 328 GGCAATTATTACCAGCTTGCAGTTTGTTAAGGGAAC 158089:295 AAATCAATCATGAAAATCTCTTTAATAACTTCTGCAG TCTTCTGAGCAGGGCAAAGCTGGGCAAGAAGAGAAC CATTACTGCTATTTTGTAGCAAAGTA CCACTGCAGCCGCATTTTGAATCGCAGG scaffold 329 TTGACCCTTTTAATGTGGCAGCCCTTCGTTGCGCGGC T C 330 ATGAACCAAGTTGTACTGCAGAGTTGGGATGACACA 17267:6243 TGAGTTTCTCGAAATGACTGAAGAATACTGTCATGGA CTAATAGTCCTCCAAAAGTGCCAAACTCTGCTTCCC AACCTCTGTGAACGCTTTGATCTCTA TGGTCTGAGGAGCTTCTGATTGTGAGCC scaffold 331 CCTAAGCTAAATTCTAGCTAATTGTAAGCCGAATAAA A G 332 AACAGTCCATAATCCTTTTGGTTTCGTCGCAGAATG 491:22100 AAAAAACCCTACAAACTGCTGCCCCTTAAGTTTAGAT CAAGCAGCCAAAAAAGGAATAACTAGAAATGCTAAT CGATGAGAGGCAGATGAATCATGAAC CAAATTTACATGGAATTTCCTTTCACCC scaffold 333 CCAGTGAATGGCGACTATTGCAGCGTACGGTGGACAT C A 334 TCATTTCCACTGTACTTGTTCCCAAGTTGGTCTTGA 121522:9070 TATTATTATGTCCTCTTCCCCACCTTGGAAGCCGTCG ATTGCAACCACTTGAGCAGCATATGGAGACACAATA ACTGTCTTCACCTTTACTTGGAAGCC CCAATACTGAGCTCACATTTCGACTTAA scaffold 335 GGGCCAAAGCAGCAAGATGGTCAGGCCCTGATAAAGT G C 336 CCCCCAACTGCTGCAGCAGCAGCAGGGGCACCTGTC 24615:2202 GTGCAAGCAACCAGCAAAGAAACCAGTCCATGCACTA TTAGCTGCAGTTTGAAAAGTTGCAAAAGCTGCAGGT CTTAGCAGTTCAGTCCGAATCAGTGT GCGAAAATTGGTTGAATTAAGATCATAA C32052323: 337 ATCATGGTTCTTGAGAAGGTTGGTACTTTGCTTAGTG A G 338 AGCGATTTTCATTTGCTGCTGTGTCATAATATAAAT 699 TTTGAGTTGCAAAAGTTGATGGGAATTTGGAAAGGAA AAATAAGCATAAATAGGAGGAATAATAAAAGGTTAG GGGAGTGTGGGTCTTGCTCTTTTCTA AAATGGGATTTTTGAGCTGCTTATGGTG C32052323: 339 GAGAAGGTTGGTACTTTGCTTAGTGTTTGAGTTGCAA C T 340 TTGCTGCTGTGTCATAATATAAATAAATAAGCATAA 711 AAGTTGATGGGAATTTGGAAAGGAAGGGAGTGTGGGT ATAGGAGGAATAATAAAAGGTTAGAAATGGGATTTT CTTGCTCTTTTCTAGAGCGATTTTCA TGAGCTGCTTATGGTGGTCTAGTAGTAA scaffold 341 AATGACTTCTGCACTTCAGCTCCTTTTGATCTAGGGT G T 342 TACTGGTAATGGACATTCAACTGGTGTAAGACCTCT 14925:8868 AGTGTGCAGCAATAGAGCCAGGTTTCAAGGAAAATCG AATTGCAGCCTCGTATATCTAGAATAAGTTTTCAAG ATCCCTTGGATCCGGAATAGGAAATT TTAGCCCACTAAAATAATTAGATGGAAA scaffold 343 GCTTCGTAGCAAGATGCAATTAGCATAAGCAGCCAGA A T 344 GTAGAGGTCTAAAGCAGACGGAAAAGACATTGGTGA 133681:2742 ATAATTTTTCTGTAGAGTATTGCTGCCTTCAGTAATG GTATTATAAAACATAGCTAAAACGGGGTCGCTTTGT CAGTGAGGTTGTTTTCTGGTGGACTT TGTGTGGCTGCAAGGCCACATGGATCTC scaffold 345 TTCATCACCATCACCATCACCACAAGTATTTCAACCA G C 346 GAATCTTCGAGCGAAGATCTTAATCTTTACGGATCC 9639:84033 CGGCGCCCCTCAGATTATTCAGCCGATGAATGTTGCT ACCGCCGAGGCTGCTGCTGCTGCAGCGGCGGCACCG TTCGGTGGTGGCGGAGCAGCAGGTAC CCTCCTTTCGGGTCAAAGAAGCGGTTCA scaffold 347 CAGCAGTCAACCCAGCAGGACCAGCTCCTATGACAAT T C 348 GCAGCTTGAATAGGGGATGACTCTTTTTCTACATCC 61482:2893 AATTTTCTTTCCAACGTTTGTATGACACCGTGGATAA AGAGTCACAATAGGGACTTTACCAACTTCCAATGTT AGATTCTCCTTGGCATCATCATTAAA TCACATGATATTTCTGTACTTCCAACAT scaffold 349 AGAGGTCAACCCTCGCATTCTTCGCGGGGAGTATGCA C T 350 GGTAAGTTACCTAGGAAGAAGGGCAACAAAGTATAT 30395:12115 CGGCTATGTTCGGCCAATTCTGCTGCAGCATTGGGAA GTCAACTACATGAAGAGCAGCAAGTATTGCATTTGT AATAAAGACCCCGACATGAAAATTTT GCAAAAGGGTATGAAGTCAATAGTCCTA C32064647: 351 GAGCTAATTTCTGGAAGAAACCCTGTTGATTATAGTC T C 352 AATTATAGGCTGAAAGTGAATCTATATTTGCAGGTG 1071 GACAACAAGGAGAGGTTAGTCTTGATTATGATTTGTT AATATGGTTGAATGGTTAAAAACTTTGGTTGGGAAT AAACCTGTAGTTTGCTTTCCTGCTGC CGGAAATCTGAGCAAGTAATTGATCCCA scaffold 353 GTGAAGCAACCTGTGAAAGCAGAGGTGCTTGGCTTCT C T 354 GTCATGTCTTCTTCATCGCGCTGCAAATGAAGAGAA 2452:1249 CTTGGCTGCTTGCATTTGAATGTAATACTCTTTAAAC TTATTAGACAAACTCTTAGTATTTGAACTTGGTTGA TCAACCGGGCAATTCCTAACTAGTTC GAATTGTACTAAAACTATAACTATTCCT scaffold 355 AAGCAGTCACACAACAAGAACCTCCACGAAAATCTTG G A 356 CCATCCTTGCTCACTAATTCAGCCAATACGTTCTTT 11436:6161 TTTAAGAAAGTCTGAATCTGTGTTCAGGTAACCATGC TCCAAGTTATCAGCTGCAAATGCTGCAGCTTTTGAG TTAACTGCCTCCTCAATGTGGTCATC CCTCCATGTCCATCAAATACACCAAAGA scaffold 357 CCTTCTCCTGCAACTGCAATCAATGAGTCTCCAAAAG G A 358 AGAAACACCATCAATCCCAACTCTCAAACCCCAAAC 4156:16965 AAACACCATCTAAACCATCTGTAAAACCTCCAACACC ATCTTCTACTCCAAGTCCCAAATTTAAAACACCATC ATCTGGTGCAGCCACTAAGTCACCTA TCGTGCAGCCACTGAATCTCCAAAAGTA scaffold 359 CCTTCTGCCATCCCATTGTCAAGTCTGGCTGAGGCAG T C 360 TGCTGCTGAATCATTTGTTGTTTCTTGATGTAACTG 43435:8325 GAAATCTATTGGATGGTGGAGACTGATCGCTGGTAGC TGAAGATGAATGCTTATTCCTACGGCGTCCAGCACC ATTATTGCTGTCTTCTTGTGTAACTA CACAGGTACATTTCTAATTGTTCCCCCG scaffold 361 ATTTGCAGGGAAATGAGCCGCTGGAACTGCAACTTCT T A 362 CAGATTCAGTGAATTTAAACATACAGAGTACAAATA 11297:60144 GCTGCTTCTGGAATACCCTGAAGAGAAAACATCAATA GTCGACTGCGCGTTCTGGATTGTTATATGCTGCTCG GTTAAAACAAGATAAAACAGGTGTCA AAGTGCACGAGTAACAGTTTCTCTGTCC scaffold 363 GCAGAGGTCCAACTGTTCGTGCCGTAACGATAGATGG A C 364 ACTCTCGTATCTCTTCCTAACATGAGTAAGGAACAA 51841:4904 CAGCAACTCAAGCATGGTCAGTTTTGTGGTTGAGCAG TGGCAAACCATTGCTGCCATGTTTGATAACGTTCAA CCCACTTCATCTACCACTTCTTCAAA TATTCTAGCAATCGTTTGCACAATGAGT scaffold 365 TTGAAGTGTGCTCGATAGAAGTAGATGTGGCCCGAGC A G 366 GTGACCACGAATGAAGCTGAAGCTTGGGAAGCAGCC 38015:40961 TTCGTTGATTCTTTCAGTGGGAATTTCAACAAGGTAT AAGAAAGCTTCAGGAGGTTTGCATTTCCTTGCCATT GTGTATGCAACTTACAAGAAAAACCC CAAGAAGACTTGGATTCAGATGACTGTG scaffold 367 CATATTATTATTATTATTATTATTATTATTTCTATTT A G 368 GCTTGTTTGATGATGATCTTCCTCCTCCTCCTCCTC 16206:63417 AACTGCTGCCCTTTATTATTTCTCCATTTCGATAGCC CTCCTGCTGCTTCGTTGGTAATGGCGGTTGCAGAGA CGAAAAGCGAAAAAGACTTGTTGCCC CATCTTTGCTCTGTTTTTGATGCTCCAT scaffold 369 CCTTCCACCTCTACGCTCCTAAGTCCTTCTCTACTCG T C 370 TCCTCTGCCACAACCGCCGAGGCTCCGCAGCCTAAA 13781:319 CTTCCCCAACCCCTTCACCGCTTCACGCCGCTCCACT TCCTCTCTTCTTACTTTCCAGCAAGCCATTCAACGT GCAACTCCACTATCTGCAATTACTAC CTCCAGGTTTGTTTCCAATGTCTAATTG scaffold 371 TCAGAGACTAAGAAACATGCCACTATAAAAATACGCC T C 372 GAAATCCCAGTCATATTTAAAGATTAACTCAAACTG 27023:20610 ATCTTGTTAATACTAAGAAATGTCACCTCACCGCAGC TTGCTGCAAATCTTCAAGTGTAGCAGAAATGTTCTC AGGCACATCTTCTTCCAGGAAGTTAT CTGCAGGTCCATAAACTGTTCAGGGAAT scaffold 373 TATATTTATATAAGAAAAAGATGAGAGAAGAGAGGAA T C 374 TCTCTATACATGTGAACCGTAGCCATTAGCCCCATT 4618:83522 GATTTAGAAAGCAGCAAAGGACCCATATCCTCCTCCA TCCATTAGCACCATAAGGGACCTTGTTCTCTGTTTT TTAAGGCAACTAAACCCAACTAACTA CTTCTTCTTCAGTACGTAAAACCATGTA scaffold 375 GCAGCCTAGCAGCACTGCTTGCTCCACGGCCACGGCC G A 376 GGAAGAATTTGCAGCCTTGGATTCTGCTCGGTGCCT 111383:2928 ACCAGATGGTGATTTTGAACCGAACTTCGTATATCTG GAGTTTTCAGCTGCCAACTGATAGCTTTTGACCAGC GAAGAACTCTTCCTAGTTAATCTTAC TCAAGCTGTCGCGCAATTATTTCCGAGC scaffold 377 GGTCATTCATTAATGTATGGTTAGTTATTGGCTGCTG C T 378 GATTTTTATTCAAGAACTGAATTCTTTTATGCAGGC 35:25795 GCACTTGTCTGTTATGCATGAAATACTTATTGTTATA TGCTTACAGCTACAGTTGCCTGGCCTTTCCCAGCCA 293 TGGTGAGTTTTCAAAAAACATTTGCA TTATTTACATTGGAATTATTCTTTCGAC scaffold 379 TGATATAGTACAGTGCGTCCATGGCGTCATCGTAGGC C G 380 GCGGCTAAGTTGAATGTGAAATTATGAGTCACAGTT 122455:2010 TGCAGGCAGACGGTGCTCCGGAGCCAGACGATACTCC GAGGCTGCACTGAATAGGATGAATCCACCGCCATGG ACAGAAACTACAATGGCAAAGATTTC AAGTAGACTATAAGAGGCAATCGTAGCT scaffold 381 TAAATTGGTCGTTTATATTAATGTTATAAAGAACGCC A C 382 TCTTCTATCTTCTAGGGTTTGGTAGTTCCCTTGGAC 13362:101120 CTAGCTTTAGCTAGAGCAGCTAGAGCGTGAACCCGGA GAAATCGTGGCTGCTTTACTGTTTTTTGGGTTTCAT CTAGTTTTTTTTTACTTCTTGCTCGT GGAAGATTTTTATGAGAATCGAAGCAAT scaffold 383 CCAGAGACCATATCTATGCGTAATACATGTAAAGGCT A T 384 GTGAAATCGAAACCATTTCCGTTTGCATCAGTTCCA 38557:23764 ATTTGAAGCAGCACAGGCAAGTGAGTTTTCGGTTGGA GAGGTATCCGCACCTTTGTGGATAAACAAGTCAGTT TGCCAAGCAAGATGGAGCAACTTTGT AAGAGACAAAATGGGATGAAAATTAAAA scaffold 385 AAAGGCTATTTGAAGCAGCACAGGCAAGTGAGTTTTC G A 386 GTTCCAGAGGTATCCGCACCTTTGTGGATAAACAAG 38557:23794 GGTTGGATGCCAAGCAAGATGGAGCAACTTTGTTGTG TCAGTTAAGAGACAAAATGGGATGAAAATTAAAAGT AAATCGAAACCATTTCCGTTTGCATC TAGCTAAAAAGTGGGCAAGACATACCTC scaffold 387 GAAGGCGAATGACTTGGCGTTGGAGGACTGAGATAGC G A 388 GCGTCCTCTCTCTGGTGAGGGAGGACCTCGTTCAGG 50091:2544 GCCTACGCAGCCGTAGACAGGATCTTTCATCCTGGCC AGCTTGCTCACATTGCTCGCCCCAAATATTTTGTGG TCGGCTTCGTAGGCCAGAGAATTAAC ACGTTTGCGAATTTCTGTGGCTCTTCAG scaffold 389 GTGATCTTCCAACATCTGTTGATTGGAGGAAGAAAGG A T 390 GCAGTTGAAGGTGTCAACCAAATCGAAACAAAGGAG 16614:72706 AGCAGTCACTGGAGTCAAAAACCAAGGCAACTGTGGT CTGGTATCTTTGTCTGAACAAGAATTGGTTGATTGC AGCTGTTGGGCATTCTCAGCTGTAGC AGCTCGAAAAACCATGGTTGTGAAGGGG scaffold 391 AGCCATCAAAGAATGCGAAATCAACAGGGAAATTGGG A G 392 AACTTAACGATGGCCACCATGAGATCTTTTATGTCT 4877:4542 ATCGTTGTGGAGGCTGATAAAAGGATAGATGTTTACA GTTCTGAAGTCACCGTCGGAAGGTTTCTCACTCGAG GTAAAGGAACCTCCATTGTCGCTTAA CTGCCATATACATCAGCGTTTAAAGGGA scaffold 393 TAGCAAAGATCGAAGCCTCACATCAACACTCACAGAT A T 394 GCACAACACTCGCAGATCGAAGAAAGGATGCCCACG 65894:5390 CGAAGCTGCCTCACATCAAAACTCACAGATCAAAACT TCTCACAATTTCGGTTCCAACTTTGCAGCTTTTCCT GCACAACAACACTCGCAGATCGAAGC CCCAGCTTCACCTCATTGCTGACAAGTT scaffold 395 CATCCGAAGTAGGATCATGTGCGCGGTTGCGGCGATG T C 396 CTCCCTCTTTCTTTATACTTCTACACAGCAGCAACT 90107:10791 GGCCCCACTTCACTGTCCTTTTCTCACAACACTCAGG ACTTAACTTAGCCTCATCAAAATTCAGCCAGGAAGG ACCCACATACACATAACATAACCCCT ACCAGATGAGATGACCTTGCTTCTTCCT scaffold 397 CAATGAAGATTCAAGACCAACATGTCAATGCCCAAGA A T 398 GCGCTGAAGACGAGCTTACTCCCGACATAGAAGATC 68873:1704 AAGTACTCTTTTATTGATCCCAATGACGAATATGGAA TCTATGATGTTGAGGAGCTGCGCAATGTAGATTGGC GCTGCAAACCCGATTTCATACAAGGC CCTTATCAGATTATGTTGCACTGAAGCC scaffold 399 AGGTTGAGACTGCAAGGATTTACAATGTTGATGATCT C T 400 ATTGCTGATGAATCAAAACAATTTGAAGCATGGAGG 3842:188176 GAAAGAGGTTGTAGCTGCTAATAAAGAAGATCGTCTC GACTCACTGGAGACTGTTCCGACCATCAAGAAACTG CGCAAAGCAATGGAGGCTCAGGCAAT AGAGCTTATGCTGAAAGAATAAGGGCTG

TABLE 8 Minor Allele Minor Allele SEQ SEQ Minor Major Frequency Frequency SNP Name ID ID Allele Allele FST (Indica) (Sativa) scaffold6803:13242 401 402 A G 0.733989 0 0.7745 scaffold543:54226 403 404 A G 0.722743 0 0.7647 scaffold281:231978 405 406 A T 0.720457 0.9722 0.2049 scaffold729:175391 407 408 G A 0.708923 0.01389 0.76 scaffold281:232029 409 410 G A 0.70327 0.8333 0.1048 scaffold2409:27009 411 412 A T 0.6646 0.8243 0.1228 scaffold25:303031 413 414 A T 0.650114 0.9306 0.2241 scaffold63:301758 415 416 A G 0.631811 0.01515 0.7037 scaffold92:214563 417 418 A G 0.628155 0.8714 0.1875 scaffold3286:29761 419 420 C T 0.6277 0.04167 0.7188 scaffold823:18400 421 422 A G 0.61526 0.02703 0.6923 scaffold1697:24776 423 424 C T 0.592909 0.8333 0.1786 scaffold414:37377 425 426 A G 0.592212 0.9028 0.2414 scaffold5405:41764 427 428 C T 0.591134 0.8611 0.2054 scaffold6803:13272 429 430 A T 0.591045 0.7414 0.1132 scaffold2317:118844 431 432 T C 0.587962 0.8514 0.1983 scaffold370:274852 433 434 A G 0.586146 0 0.6364 scaffold1014:55374 435 436 C T 0.585084 0.7581 0.1273 scaffold3831:62396 437 438 A T 0.583082 0 0.6275 scaffold2449:58347 439 440 A T 0.581874 0.6087 0.05833 scaffold1006:18102 441 442 C T 0.581751 0.03704 0.7 scaffold143:176913 443 444 G A 0.581249 0.08333 0.7315 scaffold2317:118609 445 446 G C 0.580874 0.8514 0.2034 scaffold3:20935 447 448 T A 0.576848 0.6212 0.05556 scaffold543:54256 449 450 A T 0.576198 0.7308 0.1182 scaffold360:162466 451 452 T C 0.575327 0.5882 0.03448 scaffold423:66668 453 454 A T 0.573557 0.01667 0.6604 scaffold1317:10314 455 456 G A 0.572596 0.8676 0.2255 scaffold1517:10238 457 458 C G 0.571584 0.01515 0.6471 scaffold1880:146873 459 460 C A 0.571491 0.7571 0.1339 scaffold1297:57086 461 462 A G 0.571186 0.7833 0.1552 scaffold682:73395 463 464 C T 0.570734 0.7344 0.123 scaffold92:214750 465 466 A T 0.569779 0.08333 0.7212 scaffold143:176964 467 468 T A 0.567528 0.7778 0.1509 scaffold942:90233 469 470 T A 0.566759 0 0.6293 scaffold942:89745 471 472 G A 0.566759 0 0.6293 scaffold24:306989 473 474 T A 0.565856 0.8143 0.1827 scaffold1281:68808 475 476 C G 0.564701 0.803 0.1735 scaffold1880:146829 477 478 A G 0.56444 0.7273 0.1182 scaffold3:20953 479 480 A G 0.561743 0.5938 0.04918 scaffold580:4170 481 482 C T 0.559158 0.7429 0.13 scaffold604:135874 483 484 T C 0.559151 0.8571 0.2241 scaffold1692:85945 485 486 C G 0.55769 0.06667 0.7037 scaffold1041:93642 487 488 A G 0.555826 0.1111 0.7407 scaffold1926:69537 489 490 C G 0.554742 0.9348 0.2845 scaffold4210:100547 491 492 G A 0.554584 0.9 0.2627 scaffold759:86606 493 494 A C 0.553393 0.7069 0.1132 scaffold25:425571 495 496 C T 0.553335 0.8571 0.2308 scaffold692:20843 497 498 G A 0.552253 0.8281 0.2018 scaffold2515:21370 499 500 T C 0.551959 0.8065 0.1842 scaffold48:65442 501 502 C G 0.551514 0.8784 0.25 scaffold48:65391 503 504 T C 0.551514 0.8784 0.25 scaffold3177:95787 505 506 C T 0.550219 0.7727 0.161 scaffold3681:699 507 508 T C 0.550046 0.01389 0.6311 scaffold3570:26136 509 510 C T 0.548187 0.7241 0.1311 scaffold388:236449 511 512 C A 0.546671 0.8194 0.2 scaffold763:27574 513 514 C A 0.546635 0.05556 0.6698 scaffold794:150222 515 516 A G 0.54559 0.06452 0.6909 scaffold152:25430 517 518 G T 0.545375 0.8243 0.2059 scaffold108:362803 519 520 G A 0.545191 0.7222 0.1271 scaffold388:350925 521 522 A C 0.544283 0.04054 0.6518 scaffold2218:32474 523 524 T C 0.542777 0.7188 0.1271 scaffold604:135639 525 526 G C 0.542637 0.8472 0.2281 scaffold2741:33031 527 528 G A 0.542595 0.8194 0.2034 scaffold4991:44264 529 530 A C 0.542051 0.01351 0.614 scaffold2483:94844 531 532 G A 0.541013 0.8125 0.1961 scaffold3871:24039 533 534 T G 0.540111 0.07143 0.6897 scaffold616:154319 535 536 T C 0.540002 0.06061 0.681 scaffold1005:75114 537 538 T A 0.539944 0.01562 0.6293 scaffold4991:44417 539 540 T C 0.538537 0.01351 0.6121 scaffold38:121620 541 542 G A 0.537429 0.8611 0.2455 scaffold1005:75091 543 544 A G 0.536369 0.01562 0.6271 scaffold298:209613 545 546 A G 0.534826 0.07143 0.6864 scaffold152:25429 547 548 T C 0.534254 0.8243 0.2143 scaffold1003:70848 549 550 T C 0.534107 0.02778 0.6333 scaffold839:64955 551 552 A G 0.533035 0.7419 0.15 scaffold4070:22473 553 554 C G 0.532019 0.06944 0.6731 scaffold1419:187408 555 556 T G 0.53116 0.8636 0.25 scaffold3871:24091 557 558 G A 0.531082 0.07353 0.6864 scaffold3871:23604 559 560 C A 0.531082 0.07353 0.6864 scaffold3871:23603 561 562 G A 0.531082 0.07353 0.6864 scaffold3:388526 563 564 C T 0.530397 0.5625 0.04839 scaffold4:729494 565 566 A G 0.530117 0.5735 0.05 scaffold2283:29120 567 568 C G 0.528671 0.7286 0.1404 scaffold4350:64549 569 570 T C 0.528523 0 0.5784 scaffold2283:29096 571 572 T A 0.527957 0.8235 0.2155 scaffold3469:17543 573 574 A C 0.526758 0.6774 0.1091 scaffold1022:170497 575 576 A T 0.526672 0.6111 0.07143 scaffold964:106240 577 578 C T 0.526638 0.8824 0.2705 scaffold1419:187788 579 580 T A 0.525371 0.8429 0.2368 scaffold3386:35408 581 582 T A 0.524758 0.4848 0.01613 scaffold575:241067 583 584 G C 0.524744 0 0.5877 scaffold1863:93953 585 586 C G 0.524401 0.8571 0.25 scaffold575:459449 587 588 G C 0.524202 0.8333 0.2288 scaffold773:155167 589 590 T C 0.523913 0.4483 0.008197 scaffold773:155164 591 592 G A 0.523913 0.4483 0.008197 scaffold107:154377 593 594 C T 0.522808 0.5862 0.06557 scaffold371:34271 595 596 C T 0.522699 0.02857 0.625 scaffold78:341641 597 598 A G 0.522194 0.7571 0.1667 scaffold156:85625 599 600 T A 0.521494 0.01429 0.5918

TABLE 9 SEQ SEQ SNP Name ID Upstream Sequence Minor Major ID Downstream Sequence scaffold 401 AAGGAAGAAGTTGGCAGCAAGCTCACCGTG A G 402 TTCAACTGATTCTATTTCAATTCATAAATTTTTGTT 6803:13242 GTATCCACTGAGGAGATCATCCTCGAGCGA TTTGAAAGTTGGATTATAATATTATATAGGTAGCAA CCTAGGGCTCTCGGTACTTTATTATCATTC GGGGGAAGAAGCTAAGAATTCCGGGGAT CACAATGATT scaffold 403 AAGGAAGAAGTTGGCAGCAAGCTCACCGTG A G 404 TTCAACTGATTCTATTTCAATTCATAAATTTTTGTT 543:54226 GTATCCACTGAGGAGATCATCCTCGAGCGA TTTGAAAGTTGGATTATAATATTATATAGGTAGCAA CCTAGGGCTCTCGGTACTTTATTATCATTC GGGGGAAGAAGCTAAGAATTCCGGGGAT CACAATGATT scaffold 405 TCATGTTACTGCTGATTATCGTCACCGATA A T 406 CTGAGTGATTTAAGAGAACTTGCTTCAGCAGAGAGG 281:231978 ATTGCTTCTAACCTTTCTACATTGTGGTTT CCTGGATACTTCACGCTCATTTACACAAATATTCTC TTTTGACCTGGCTGCAGAAAGTTGAAAACA GAACATCAACCTGACTGCCCGGTAACTT GAGTAAGAAT scaffold 407 CCAGCAAAAGTGGCTCGTGCTGATGAGAGT G A 408 TCAGATACACCAGTACCATCCACAATAACCCTGTGG 729:175391 CGGGATTGCTTTTCCTGAAACCAGAGATAA CAGACAAGTTCTCAAGCTAGTAGGAATGAATGTCCT CTCTCACCCGGGCCAAAGAGGGGTGTTCTG CCGCAAATTGAAACCACTGTTCGGATCT AAACATGCAG scaffold 409 TTGTGGTTTTTTTGACCTGGCTGCAGAAAG G A 410 CTCATTTACACAAATATTCTCGAACATCAACCTGAC 281:232029 TTGAAAACAGAGTAAGAATACTGAGTGATT TGCCCGGTAACTTATCTGATACTACAGAAATTGCAT TAAGAGAACTTGCTTCAGCAGAGAGGCCTG TTTGTTCTAAGCATTGCTTTCGGTTTTT GATACTTCAC scaffold 411 CGATGTGTGGGTTTTCAGATCTCTTTTAAG A T 412 TAAGATTAAAAACATAAACAAATATGATAACACTCA 2409:27009 GCGTAAGAAAATTTTAATAAAGGAATTGAC TGCAGATTACAAGGAAAATGCACATGGCCACTGCAG TATATAGGCAGGCAGACAAGAAGATGGTGG GTAACAATGTTTGACTTTTTGTTAATTA CTTCACTTTC scaffold 413 ATGAAGCAGGCCGGAGAAAAGACGTTTTTC A T 414 GAAGAGTTGCGAAGAGAACTCGCTTTTTGCACCTTA 25:303031 CTGTTTTAAACAATCACTAAAGTTAGGAGT ATAATTTAACACTCAGCATTATTTCTTATTCGCAGA TAGGAGAACTGAAAAACAAGTATGAGATGT GAAAGAGAGAGAGGCCTCTTCGGATGGA AATCAAATTA scaffold 415 TGCGACCCATAGCCTGTGAATCAGAAGATA A G 416 GCAAAAGCTACATCTTCCGGGATGTTCTTGTCAAGG 63:301758 TAATGCTGATTGCGCCCATATCATGCAAAA TGATGGCAGACCATCTGTATGTAGCAAGACGAAAGT TATCTTCTGCAGCAATTGTTTCTGCCCTTA GAGAATATTGAACAGCCATAGTGCACCT TTCTTGATTC scaffold 417 ATTGTTGGTGCATATGAGGAAGGCCACCTG A G 418 GAAGCTCCCCATGACCCTAAATTCCCCCCAGGTTGA 92:214563 CAGGTCCATAATATCCTTGCCAGTACATTG TACAAAGGCAATGAACCTTGAAAAGTGGACCCAGGA GCATAGCAAGCCCACCACCATTTGCACTCG AGTCCCAGTTGTGCTGTATGGGAACCAA GTGCAGGAGG scaffold 419 GCCACAACTCCCACCATCTTCCTCAGCCAC C T 420 ATATGTGAAAAAAAAAGAACAGAAAATTTTCAAAAT 3286:29761 CCTGCAGCTTCATTTCTTCTAGAAGCTGAG TGGAAGATTACAAGTACTGGCCATAAACACCAAACA GAAAAACATAAAAGACACAATTAGGAAACT CCAAAATTCTCAAGAGTCAGATCCTAAT AAATTAAATA scaffold 421 TAGAATGGTTTTGCTATTTGTATATGAATC A G 422 TACGCTGATTCATGCAAACAAATCTTCTCAAGCTTC 823:18400 ATGTTCACTTGAGTAGAAGTCTATACTCAG GTAGGCCAATCTTCTCCGAGAAGCAAAGGGTTCATT CAAAAGAATCTGAAGCAATCACTTATCTGC TCCATTACAACCCGGAAATCTATCATGG TCCCAGTTTT scaffold 423 CCAAAAACTTTTCATTTAACTGTTCTCATG C T 424 AGCTGGTGCCTGGAAGTCAGTACTAACTGATAAGCT 1697:24776 TTAAAACTGTGGAACAAGGAACGAGTAGCT ATTCTTTTCTTTCCTTCCAGAGTGTCTCTTCTAAAG GCAGCTGCGAAAGTTTTGCAGGTAAATTTG TGATGGAACCTTGGAGAATCGGCCGGTC AGTTTGATAA scaffold 425 CGCCCTGAGCACCCTTAATGGGAGTGGTTG A G 426 TCATGGCATATTTCGCTATGTTTCTTCTGCGTCTGA 414:37377 GAGCAGACCTCTTCTGCTGCAGCGAATGGA ATTTTCGACAGTCCGTTCCGTGCTGTCCCTTTCCCG GTTCGTCGATGGTTTGGGCCTTCACCGTTG GTCCGAAGCTGAACTCGCCGTTAGCGTT GCGCACTGTC scaffold 427 CCAATCAATCTGCAGTGACGAACCTCAGCT C T 428 GCTTTTGCTTATCACCAACATCAACCACTGTCGTCG 5405:41764 GAGACTGAGAAAACCAAACACAAATGACAG CAACCATCGTTTATTCAATGCGCACTGACGAAACAA TATGTTTTCATGTAAGCTCTCCCCAAATCC GGCCACCGCTTCCTCTCCACTCTCTCAG CAGCCCCATT scaffold 429 GTATCCACTGAGGAGATCATCCTCGAGCGA A T 430 TTTGTTTTTGAAAGTTGGATTATAATATTATATAGG 6803:13272 CCTAGGGCTCTCGGTACTTTATTATCATTC TAGCAAGGGGGAAGAAGCTAAGAATTCCGGGGATCC CACAATGATTGTTCAACTGATTCTATTTCA ATTGAGTGCGAAAGGCGGTGCTGTTCTC ATTCATAAAT scaffold 431 ACCAATGAGAAAAACAAAATTAGTTACACT T C 432 TACCTGAAGTTTTATAGGATCAGGATTTGATCCATC 2317:118844 TTTTCGGTTTTAACATCTCTAAACTTTAAA AATAATGTCAATAGCTCCATTGATCCGGAATTGCTC CCAATAAACACGTTCCAGCATTATAAGGGT CCAAGAGTCAGTGAAGTACCAACAAATC GTTCGTTCAG scaffold 433 AATATCATTTGCTATCTTGTAAAGCTCTAA A G 434 GACACAAAATATAGCTCAATATAACTATACCGAATC 370:274852 AGCTGCAGGTAGATTTTGTGCCTCCTTTCC AACATACAACAAACACAATCCAACGCACACTACAAA CATTCCAACTGCTTGAGCACCCTGAAATAA AGGATTCAAGAATTATGTCTCCGACTAA GAAACAGACA scaffold 435 CTATTAGACTGTAGAGCATTGCATGAAAGG C T 436 ACATTAGGCAACTCCTGCTGAATGGCAGTGCTTACC 1014:55374 CTTACTTTATTGGTTTAAAAAGTATAGTTC TGTTCCGGAAATGTATGTGTTCACACAAAATCAGGC GGGTAGATGGATTCTGCAGATAAAGTTTCA TCAGTATGACCTTTATAATGTCAATTAG TCTTTCCCAT scaffold 437 GAAAAAACACCCCTCCAGCCTGCAACATCA A T 438 GTTGAGAAACAAACGAAACATTTAAATCCAAGGAAC 3831:62396 ATTCAGTTGACAGCTTGCAGGACTCGAGCA ACGCAAGTCACAAATGCCTTGAACCGACACCATTCT AGTTTCGTACCAGTAACTCTGCAGATCACA TCCCAAGATAAAAATAACACGATGACAT GAAAGGTATC scaffold 439 CGATCATTCGTACCTGCAGTTGAAAGTTGA A T 440 ACATGATGTTACTTTTTCAGTAACACTACCCCAACT 2449:58347 ACCTTTTCAAGTTCAAATGTTGATGAATTA ACTTCCATTTAAGGTTGGTAACCCAATACTTCTACC ACAATACAAGGAGACATTTGATCTTCATCC TTCATCACATGTTGATATTTTTCGATTC ATGTTTGTTG scaffold 441 TGTAAGACCAACGTGAACAGAGCTAAGGAC C T 442 TCCACTAGGATTTTCCATAGCAATGCTTGGCTGCAG 1006:18102 CATAAGAAGTTGAAGGCCGTTGAGGAACCA AGTGACATGCTTATTCGGAAGTAACCAGCGTGAAAC GGCGAAACACTTGTCGTAATGAGTGAACGT CTGGTTAAAATAGATGATAATATGGGTT CGTCGTTTGG scaffold 443 CGTAATGCTGTTCTTGCTGTTATGTCTGTT G A 444 CAGGATAATTCTAGTAAGCATAATGCTTTTCTTATG 143:176913 TATCGACTTCCTGGTGGTGATCAATTGCTT CTTTTTACTTGTGATGAAGATCGTGCTGTTAATTAC GTCGATGCACCGGAGATTATAGAGAAGTTT CTTTTTACACATGTTGATAGAATTACTG TATCTTCGGA scaffold 445 CGCTAGAATTGTCGAGAAAAGTTTCTTTAG G C 446 GAAAACCATGATTTCTCTCTTTGCTGCATCATTCAG 2317:118609 TCGGATCTTCATCTATACTTGGAAGACCTG AAAAGAAAAGACAAATATGTGGAAAATTTAGATAGT GATTAGGCCCCAAATACTGCAGCCTAGATT TCAAAGGGAAGTTAAAAGCTGAACTAGC TAAGAGAACT scaffold 447 GACTCCTCAACCTTTGATGGAGACGAAGAA T A 448 ATCCGGGCATCATTTCAGTGCCTTATTTTATTCTTG 3:20935 GATGAATTGTACCAACACTTAGTTTAAAAC GTGTAAAGATTAAAGATTAAAAATCAAAAATCAAAA AAAGCTTTTTACTAGATTTTCTAATCATTA ATCAAAATTCTTTCAGAAGATTTCAAGC TTATTTTGTG scaffold 449 GTATCCACTGAGGAGATCATCCTCGAGCGA A T 450 TTTGTTTTTGAAAGTTGGATTATAATATTATATAGG 543:54256 CCTAGGGCTCTCGGTACTTTATTATCATTC TAGCAAGGGGGAAGAAGCTAAGAATTCCGGGGATCC CACAATGATTGTTCAACTGATTCTATTTCA ATTGAGTGCGAAAGGCGGTGCTGTTCTC ATTCATAAAT scaffold 451 TGGAAACAGGAATAGATGCCCCACCGGAAC T C 452 CGCCGCTTCTTCTCTTCCTTCAATTGTTTCTTCATA 360:162466 TTTCTTCTGTATTTTCACCTAAATCTCTGG AGAAGCTTTTCCCTATATTCTAACTCATCATAATAG GCAAATCCTTCACAGCTTCTGCCATTTTCT GCCTTCTTTTGAGCTTTGGAAAGCTTTG TCATAATTTT scaffold 453 GAAAAAACACCCCTCCAGCCTGCAACATCA A T 454 GTTGAGAAACAAACGAAACATTTAAATCCAAGGAAC 423:66668 ATTCAGTTGACAGCTTGCAGGACTCGAGCA ACGCAAGTCACAAATGCCTTGAACCGCACCATTCTT AGTTTCGTACCAGTAACTCTGCAGATCACA CCCAAGATAAAAATAACACGATGACATC GAAAGGTATC scaffold 455 GGAAGTAAAGCCAAACTAGGCCAAGAGAAA G A 456 CAGTGTGCCAAGGTGTGTTCCTGCAGGTATTGAGCT 1317:10314 AGGCGAAGGAGATGGAGCAATGTAGCATCC TAAGAAGTTGAAAATGTCCAATACACCAGATAGGAC ATAAAAGATGGAACAACTAGCATTAAAGAG AATGGACGATCTCCAAAGCTTCCACGTA CTCTGTGACA scaffold 457 CACATCATAAAGAGTATCACCAATCTTTAG C G 458 ACTTCTTGACAGTGTTCGCAGCCAAAGGTGCCCGTG 1517:10238 CTTGATGGCACCACTTCTGTATACAAGCAT TGCTTTCGTTTACTGGCTGGCCATCATTGGTAACTA TTTACCCACCAAGCCTGCAGGTATCTCGTT ATTGTTTCATCAGAGGCATAGTTGGTGG CAATGCACAA scaffold 459 TACTAAAAATCTGGCCCGACAATGACGAAT C A 460 GCAGGGTAGGGTAGAGAGCAGCAGCTGTACTATGTT 1880:146873 TCAAATGAGTAATTCATCCCGGAAAAAAGA TACCCAAATTTGAAGCCACCAGGGGTAGGGTGGGTT GCAATAAAATAATTTCTTTAACAAAAAAAT GGCTTGCTCCAAAAGGAAAACCTTGTTG CCTGATCACA scaffold 461 GGTGCCATGAACTACCGGGATAGTTCCATA A G 462 GCAACCAGATCAAGAATCAGTCAGTCCCATGAACAT 1297:57086 TCTCATCGCATACAATTGATTCAAGCCACA ATTTCATTATGTTTAAATAGTGAAATAAAGAGTCAC GGGCTCAAATCTCGAAGGCATCAGCAGTAT ATCCCAAGTTTTGCGTATCTATAAAATA ATCACAGCTG scaffold 463 TTCTACTTTTCCCCTTCACACCTCCCACAC C T 464 CGCTCCTCGCCGCTGCAGATTATCTCTCCGATCGGG 682:73395 CCCCACCGAGACTTCACTTTCATCATCAAG TACACCTCCACGTCTATATCGACCACTTCGCATTCG GTTCTCGCCTACAACCGCCTCGACTCGCTG TCAATGGCTCCACTGATGTGGATCGTAT GCCGCTGCCT scaffold 465 TGTATGGGAACCAATATCAGTCAAAGGCCC A T 466 TTTTTTTAAAGCAAGTCAACATTTATTTACCATTTT 92:214750 AGTAACAGCTGATGGCAAGCTTGAAGATGA GGAAGATGTATTATCAATAAGTTAAAAAAAACATTC GGTAACTGGGCGAGTATAGTGAGACTGCAA CCAATCTCCCATACCTGAATGATAGCCG CATAGATTCA scaffold 467 CAATTGCTTGTCGATGCACCGGAGATTATA T A 468 GAAGATCGTGCTGTTAATTACCTTTTTACACATGTT 143:176964 GAGAAGTTTTATCTTCGGAACAGGATAATT GATAGAATTACTGATTGGGTGAACAGCTTCAGATGG CTAGTAAGCATAATGCTTTTCTTATGCTTT TTGTGTTAGAATTGATTAAGAAAGTTTG TTACTTGTGA scaffold 469 GGAAACGAAAGGCACCACGCCAAACGTGAG T A 470 GGCCGAGTAACACGCAGAGCAACCCGGCCACTGTCT 942:90233 CGCTCCAGCTGCTTGAACTGACACAGAGAA GCACTGCCCAGGAACCCCAAAGTCTCCCTCTCAATT TCCACACAAGACAACAATGGAGCCCCATAG TTTCTTTCTATAACTTCTTTGCATTTTT CGAGTTACCT scaffold 471 CTTCGATTTCTGAGCTTACTAAGTGAGCCA G A 472 AACCATTTGAAACAAATAGGTTCCTGATAGAAAGAA 942:89745 TGCTGTTTGACGTGGCTTATCTGCAGTAAA GCCATCTCACATATCTTCTGTTGCCTTGGCAGATTT CGGTCCACTCCACTTTACAAGGTATTTTCT TCAGAGCAATGTACTTCATCGTTCAATG TAAAGTTTAC scaffold 473 TAACGTTTCCATTCTTTATGTCTTGATTTT T A 474 TTGTTAGACGATTTTAGCTTCTACGAAAGCCGAGAA 24:306989 TTGCACAGGTTGGATTAAAGCAAGGACTGG AAGGTCCTCCTAGCCAAAAGAGCCATTAACATCAAG AAATGTTGAATATATTCAAGAGTTACACAC CCTGCAGCAACATTGAAGATGGAAACCA CGAAGACTTC scaffold 475 ACAGTACTAATGGAATCAACGGAGGAGATG C G 476 TGGTACTACTTGCAAGGAAGAAGAGGCAGGTACAGA 1281:68808 ACGGTGTTTGATTCTTCATCAATCGGTGAC AAACGACACCAATGATGACACAAACGACAACTCGAA GAGGGGGCTTTGGAGCAAATATTTCAGTAC AAACTGCAGATTTCTTCCAATCAACAAC ATGGGAAAGA scaffold 477 AAATACTTCAATATAACAAATTCCATAGAC A G 478 AGAGCAATAAAATAATTTCTTTAACAAAAAAATCCT 1880:146829 GAGCCTATGTGCCATACTAAAAATCTGGCC GATCACACGCAGGGTAGGGTAGAGAGCAGCAGCTGT CGACAATGACGAATTCAAATGAGTAATTCA ACTATGTTTACCCAAATTTGAAGCCACC TCCCGGAAAA scaffold 479 GGAGACGAAGAAGATGAATTGTACCAACAC A G 480 TGCCTTATTTTATTCTTGGTGTAAAGATTAAAGATT 3:20953 TTAGTTTAAAACAAAGCTTTTTACTAGATT AAAAATCAAAAATCAAAAATCAAAATTCTTTCAGAA TTCTAATCATTATTATTTTGTGAATCCGGG GATTTCAAGCATTGTAGTAAATCTTTAT CATCATTTCA scaffold 481 GATCATAATGAGTACTTGATCTAGCTTGAG C T 482 TGGTAGTTAGATTCAGAGTGAGAACAAAGGACTCTT 580:4170 CACTGTTCATCCACAAGTTGACAGAAGCTA TGTTAGATGGCCATAGAGTAGTAAACACAGACTGGT AAACCTTTTCCTTCAAAAATCAGGCTGCAG CCAAGAGATTTACAAACCGTATTAATAT AAGTAGACAA scaffold 483 ACCAATGAGAAAAACAAAATTAGTTACACT T C 484 TACCTGAAGTTTTATAGGATCAGGATTTGATCCATC 604:135874 TTTTCGGTTTTAACATCTCTAAACTTTAAA AATAATGTCAATAGCTCCATTGATCCGGAATTGCTC CCAATAAACACGTTCCAGCATTATAAGGGT CCAAGAGTCAGTGAAGTACCAACAAATC GTTCGTTCAG scaffold 485 AAAAATAGTTTTGTTATATTATATCTTCTC C G 486 AATGCAGTGATCATTGAGGCAGATGCTTTCAAAGAA 1692:85945 ATGGAAAATAGCTAATAGTATTCATTTGAA TCAGATGTTATCTACAAAGCCCTTAGCTCTAGAGGC TTGAAATGTTGAACAGACCATTCTGGGCAG GAGCTGCAGG scaffold 487 TATATAATATATATATATAAGATAATTAGA A G 488 CACAAAATAGTTACACCCAAAGCAAATGTTGATATG 1041:93642 TAACATAACATGTAATTAAGGATTAAGCAT ACCAAGCAAGGTAAAAAATATGGAAATCTGTTATTT GAAATTATTAATTTTAATTTTAACATACCG CATAATTATAAGGTTAATATGTCATTAA GCAGCCAATA scaffold 489 ACAATTGAAAAAGTTGTAATTCATTTATTG C G 490 GCCATCTTTTTCACTTTTTTGTTTATTGTATTATAG 1926:69537 AGGGATGGAGATCCCAACATAGAGTGAGCT TATAGGTACGTCGTAGAAGAAAAATGAGAAGAAGAG CCTTACCATCTGACCCACCCCTTTGCAGCT AATTAAGGAATAGGTGATATTATTATAT GCAGAACATG scaffold 491 GCTTGAGGAGAGAAGAGAGAGTAAGAAGGG G A 492 AGCTCCATGGCCATAGTAGCTAGCTTGATCCGAGTA 4210:100547 GAATGGAGCAACGATCACGTTCTGACATCA GCCTTATCAGACGGCAAGGCCTCCAAATATGGTATA CACCCTTGATGGTACGGTTGTAAGCAACTC TTGAGATCAAAGAAACCCATTCCTACTC CGGAGTAACC scaffold 493 GGGGAGATAATTGTACGACATTCGATGTTA A C 494 TGTGGTGTTGAATCCGGTGTCGTTTTGGCCCCTGCT 759:86606 TGTCGTTTGGTGCAGTTGGAGATGGTGTGG GATTATTGTTTTAAATTACTTCTACTATCTTTTCTG CAGACGACACTGCAGCCTTTAAAGAGGCAT GACCCTGCAGCCCCGGATTAATGTTCCA GGAAAGCTGC scaffold 495 CCAATCAATCTGCAGTGACGAACCTCAGCT C T 496 GCTTTTGCTTATCACCAACATCAACCACTGTCGTCG 25:425571 GAGACTGAGAAAACCAAACACAAATGACAG CAACCATCGTTTATTCAATGCGCACTGACGAAACAA TATGTTTTCATGTAAGCTCTCCCCAAATCC GGCCACCGCTTCCTCTCCACTCTCTCAG CAGCCCCATT scaffold 497 ATATTTAGCCCAAATGAAAAATTAGGAATT G A 498 CTTTTGGGGTGTTATTAGCAAATAATTTTAAGCTGA 692:20843 TTTCCTTTCACCTTTGATTTTGATTTTAAA ATTTTCTGCAGCTCTTGGCTGAGGACCCATCTTTAA ATGTTATAACATTATGGCCGGCTAACTTAG AGCGATTCAAGTCACATAAGCCTAATGT CTATCGATTT scaffold 499 AAACGATCTGACGCCCTTCATCTTGATCAA T C 500 CCTCGCCCTATTGAGCCAATTGCAATCTCTGCAGCT 2515:21370 TCTCAATTAAACAAGATTTAGCTGAGTCCC TTTGGAGCTGGAACTTTCAGCGCCATAACTCACCAA CTTTACAGTATTTGAGCCTTAGATCAATTG CGCCTGTTCCTTCACCAATCCCAGATCT AGATGTCGTA scaffold 501 TTTCTTCACCGTACATGTATAAGGAACAAC C G 502 CCAGCGGGCAAGTTTATTCTGAGGAATCTGCAGAGA 48:65442 CGGTCATAGTTTGAGAAGCCACAACCACAG TAAATTTCATAAATTTGAGGAATAAGTACCCAAAAC ATGACGCATCATCACAGAATTCAACTGCCA GAAGAAAATCCATAAATGATCATTGGAA CAGGATGACC scaffold 503 CAGGAAGAGGAGGCTTGGTTTGCTGGTTAG T C 504 ACAACCACAGATGACGCATCATCACAGAATTCAACT 48:65391 CTCCATCAGAAGATTTGGTCTTTTCTTCAC GCCACAGGATGACCGCCAGCGGGCAAGTTTATTCTG CGTACATGTATAAGGAACAACCGGTCATAG AGGAATCTGCAGAGATAAATTTCATAAA TTTGAGAAGC scaffold 505 TACCCCTCCCGGACTTCCTATGATGCGTCT C T 506 TTCCCCCTTCCGGCGTATATATCGGACCAGCTCTCC 3177:95787 GCAGCGTGTTTTTCAGGCTCGGAATCGTCG ATCAGCATCTCTCTCACGCACGCTACGTGTAGATTG ACCTGGAAAACGAGGACGAAGACGAAGAAG TACTTCTTGCACTTAGACCGGTAGCTCC AAGTAATGGC scaffold 507 AGCCTCATTTGGCTCGATTTGAACAGCAAT T C 508 AAGCAATTTGCATTTGTGAGAAATGAGGGTGGAACA 3681:699 CAACTCTCTGGCACTGTCCCCGCCGACTTG GCCTGCAGGGGAGCCGGAGGACTAGTTGAATTCGAG CTAACCAGGCTGGCCTAGTGGTTCCCGGTA GGTGTTCGGCCTGAGAGACTAGAAAACT TTGTTTCTGG scaffold 509 TCTACTTTTCCCCTTCACACCTCCCACACC C T 510 CGCTCCTCGCCGCTGCAGATTATCTCTCCGATCGGG 3570:26136 CCCACCGAGACTTCACTTTCATCATCAAGG TACACCTCCACGTCTATATCGACCACTTCGCATTCG TTCTCGCCTACAACCGCCTCGACTCGCTGG TCAATGGCTCCTGATGTGGATCGTATGT CCCGCTGCCT scaffold 511 TAGAGAAGAGAAACTGTAATGCCTACCTAG C A 512 TTCAAACCAAACAAAGAACCGGAACTTTCCTTATCC 388:236449 TTTCACTCAAGTAAGAAGAGTCTGATTTTA TCATCATCTTCATCAATATCACTGTCTTCTTCACTA CAGTTGAAGACGCTGCTGAACCCTTGGCAC AGCAAAGCCCCAATGCCCAACCTTTTTC TAGCTTCCTT scaffold 513 TCGGCGAGCAAGTATGTGTAGGTGGATGAT C A 514 TGTTTTTAAACACCCTAACTTGGTCGACTTTACCGG 763:27574 TCCTTCTCAAAGAGCTGACGGAAGAGGAGC ACTCGATAAAATCCTCGAAGAACAATTCAACAAAGC TTGCCAAAGAGATGAGACGACGTCGTATAA TGGATTAGATCCAGTAATGGTGAAGACT GAGCAAGTCG scaffold 515 GCCACCAAATGGGGGCATTGAGGCCAGGCT A G 516 ACGGGATCACAGCCAACTGCGTAGCCCCGGGGCCGA 794:150222 TTGGGCATACGCGCGGGTCAAAGGCTGCAG TCGCAACAGATATGTTCTATATGGGAAAGACTGAGG TGGAGTCTATGACGCAGATACTTGCAAAGG AACAAATTCAGAAAGCGGCGGAGGAAAA AGTTGAAGGG scaffold 517 ATATAAAATTCAATGCCAAGTGATTCAAAA G T 518 TGTACGGTCATATTTCTTAAAACAAATAAATAAATA 152:25430 CCGGTTTAATCTTCAATAAATCTTTATTAG AAATCACACAAGCCAATTGGAAAGAGGCTATTCAAC TAATGGCTTGCATTCTTCAAAAAGAATCAA TTTATACAATATAGACCTATAATGTACT CCTTTACAAT scaffold 519 CAAAGTACCACAGAGCCATTTCCAACATGC G A 520 AACCAAAAGAGCCCAAGTAATACAAAAGCAAATGAC 108:362803 CCAGCGTAATCACTAGAGTAATACAGTTCT ATGAGCCCATAAAATTTCATAAGTGGTGCCATTCTG GCAGAGGCAGAACTTCTCTCCAAAATCTTG CCGGTAGATATCCATTTGGGTTTTTCCA CATACTGTGA scaffold 521 ATCAGTAACCAGATTCACCCAAAAAGCTGC A C 522 GATATCATGTACCTGAAAATTGACAATATGAACAGA 388:350925 ACTGGTATCATACATTCGGTATTCCCAATG ACTATATAAGTTGCTCAACAATGAGATATTTCATAT CTGCAGTCAAGAATATGGATATAACCTCTC AAGAAAGGGTATATATGCAGAACTAAGA CAACATTTGA scaffold 523 CTCCTGTGTACAGGCAGTACTTGAAGATGA T C 524 ACCTTTCTACCAGGTAATCAAATTGGATACAACAAA 2218:32474 TGGAACCTCATCTTAATTAATTGTTCCAAT GTAACCAAAACTCACAGGGTTCTCACTTCATGGAAG CCCACAAAAACTTTATGGAAAAGTTTGATT AATTCCAAAGACCCTTTACCCGGCCTTT ACCCTTCCCA scaffold 525 CCGCTAGAATTGTCGAGAAAAGTTTCTTTA G C 526 GAAAACCATGATTTCTCTCTTTGCTGCATCATTCAG 604:135639 GTCGGATCTTCATCTATATTGGAAGACGCT AAAAGAAAAGACAAATATGTGGAAAATTTAGATAGT GGATTGGCCCCAAATACTGCAGCCTAGATT TCAAAGGGAAGTTAAAAGCTGAACTAGC TAAGAGAACT scaffold 527 AATTTCGATCAGGTTGCAGCCAACTTTAAA G A 528 ATTCCAGTAAAAAAACTTGATATTTATTTTTCAGGG 2741:33031 CAAAATGTCTTTTGAGTTCTTACATCAATT CCGGGTCACCATTTCTCTGTCGATGGACTACAAGTT TGTATGAATAGGTTCACCTGGTCAGCAGAA CTAGATTCTTCATGGAACAACCTTTCAA GAAGAAATCT scaffold 529 GCAACATACATATAATTAATGTCAGCCGGT A C 530 TCATTTCTAGTTGGAGCAACAAAGATAATATTAGAT 4991:44264 GATAAAAACATTTCTATCAATAAATTTCTA ATCATCCAAGGAGATAGACACATATGACATTGATAT ATTAAGAACATCAAACACTTTGACCATTAC GTGTTATTACGTTTGAAGACCCGAGCAT AAATAATAAA scaffold 531 CTTAGGGCTAATCCCTCCAACCTGCATCAA G A 532 CTCACTTTAAGTCCGGTCTCCTTTCAAACACAATTG 2483:94844 CAAAACAATGCTAGATTTTAAGAAATCACA AGAAAGCCTGTCGAATAGACAAGTCTTCGGTGATTT AACACATTAATAAATTTCTTTGTAGCATCA CTTGTCTTACTTTATCTGTCTGCATTAT ATTGCAGTTT scaffold 533 ATAAATAAAGGCTAAAATGAGTTGAACTCA T G 534 TTGATTTATGATGTTCTTTGACATTCTATAAAGATA 3871:24039 ACACCACAAGAGTTTGTGGACACACTACAT AATCTATTTGTGCTCATATCTATCAAATATCTTCCA CAAATGGGCCACAACATCTTTTACATTAGG CCTTACCGGAGATATTAATATGTGAGTA AAAATTTACA scaffold 535 TAGATCCACCTCCAATGAGGGGAAGAAAGC T C 536 AGAATTGTAGCCTGTTACAAAAATTAGGAAAGATAT 616:154319 TATACTTCTTAGCAAATTCTGCCCACCGGT TATTGACCAAAAATCACAAATTTGAATACATACGTA TTAAAAGTCTATCCTCTGTGCCAACCAATG TCGATCATGAAAAAACAAGTTTATCATG CAGCAGATTT scaffold 537 ATATTATTTCCATCCAGATGTTTCCAGATC T A 538 AACTGGGCATATAGTAATAACCAACTTTTATCAGTG 1005:75114 CGGGTATTATAAAAATGCAAGTTAAAATCT GAGCACTGGTCATCATCTCATTCCTGCAGCAGGAAT TGCTAATATTAGATTGAGAAAAAGATGGCA TCTGGTTAATATCACATACAATATCTCT TTGAAAAGGA scaffold 539 GACACATATGACATTGATATGTGTTATTAC T C 540 CAGAAGTATTTGAGTCACACTTCATCAGTTTAGTGT 4991:44417 GTTTGAAGACCCGAGCATAGTTTATTGAAA AAAAACAAGATCCTTACAGATACTGCAGCAACAGGA TTAGCCAGCTGATCAGAAAAGTTAGATATG TAATAAATCCAACACTAACATGCTCCTC AGAAAACACA scaffold 541 ACTATGTCTTCTAAGGCGATTTTGTTTCGG G A 542 ATGAATCTTTTGTAGGCCTTGGACACCTTTAACACA 38:121620 TTGTTTAGGCGACGCGACCATGGATCTTCT GCAGTTATATCTCCGGTCTACTATGTTATGTGTTAC CGTATGTAGTACTATTAGAATGTTTAATCT GTCGTTCACCATCTCGGAGCTGATCATG GTTTTACTTG scaffold 543 ATGTAAGGAAATAAACCTATGTAATATTAT A G 544 AAAAAGATGGCATTGAAAAGGAAAACTGGGCATATA 1005:75091 TTCCATCCAGATGTTTCCAGATCCGGGTAT GTAATAACCAACTTTTATCAGTGGAGCACTGGTCAT TATAAAAATGCAAGTTAAAATCTTGCTAAT CATCTCATTCCTGCAGCAGGAATTCTGG ATTAGATTGA scaffold 545 CATGATAAACTTGTTTTTTCATGATCGATA A G 546 AAATCTGCTGCATTGGTTGGCACAGAGGATAGACTT 298:209613 CGTATGTATTCAAATTTGTGATTTTTGGTC TTAAACCGGTGGGCAGAATTTGCTAAGAAGTATAGC AATAATATCTTTCCTAATTTTTGTAACAGG TTTCTTCCCTCATTGGAGGTGGATCTAC CTACAATTCT scaffold 547 AATATAAAATTCAATGCCAAGTGATTCAAA T C 548 GTGTACGGTCATATTTCTTAAAACAAATAAATAAAT 152:25429 ACCGGTTTAATCTTCAATAAATCTTTATTA AAAATCACACAAGCCAATTGGAAAGAGGCTATTCAA GTAATGGCTTGCATTCTTCAAAAAGAATCA CTTTATACAATATAGACCTATAATGTAC ACCTTTACAA scaffold 549 AGCCTCATTTGCTCGATTTGAACAGCAATC T C 550 AAGCAATTTGCATTTGTGAGAAATGAGGGTGGAACA 1003:70848 AACTCTCTGGCACTGTCCCCGCCGAGCTTG GCCTGCAGGGGCCGGAGGACTAGTTGAATTCGAGGG CTAACCAGGCTGGCCTAGTGGTTCCCGGTA TGTTCGGCCTGAGAGACTAGAAAACTCT TTGTTTCTGG scaffold 551 CCAGAAGTATTCCATGTTCATTTGCACTAT A G 552 TATATTATATTATAAATCTCAAGAGCTGCAGAGATT 839:64955 CGACCTACATCATTGAAATGAACCAGGAAC GAAAAAAAAAAAGTCATACCCTAATTACCGTAGCAT AAAAATATCTTGACTTAATTAAAACAATAT TCTTGCAAGAATCATTATCAATTACAAC AGATATATAT scaffold 553 TGTGAAAACCTTTCCGTGGTATCAATCCAA C G 554 TTCTCTCACACAAGCATTCTTGGGGATTGCATAAAA 4070:22473 TACTTTGGTTTTTGCTTGCAGTCACCCAAT ATAATCTTCCTCCTTTGGCCTGTCTGCAATTACTCT TGCAGTTGAGTTACCGGGGCTAATCAAGTC GCGTCGACTTGGTTGTCCCATCCTTTTC ATCGCAACTT scaffold 555 GTTACACCATGATGGTGAACTCTCCGGAAC T G 556 TAACATTTAATATTGTACTAATTCTAATTACACAGA 1419:187408 TTGGCCATTGGACATATTGCACACCTACAA TACCTTCAAATTTCTGTAAACTGGCTTTGCATACAA ATCAAACTTTGGAATAAGACAACTATCAAC ATGATCAATACCAAGAAAGTAACGATCG AATTACATAT scaffold 557 CACTACATCAAATGGGCCACAACATCTTTT G A 558 TATCTATCAAATATCTTCCACCTTACCGGAGATATT 3871:24091 ACATTAGGAAAATTTACAGTTGATTTATGA AATATGTGAGTATGCTCAAATAATATGACCAGAAAA TGTTCTTTGACATTCTATAAAGATAAATCT TATAACAAAATCAATATTCATCGACTAC ATTTGTGCTC scaffold 559 CCAATTGTTTCTTCACAATACCACACACCT C A 560 CAAATCATTACCTTTACACAAGGGTTGATAGCAGAA 3871:23604 TCTCCACTGTTTCTTTCTTGGCCTGCAGAA ACATCAATGATGCTGTGTCATAAGGGCTAAACACAA GGATGCCATACATAATTAGCTCCAAAATAA AGTAACGGATGTCAATGGAACAACTACA AAGTAAAAAA scaffold 561 GCCAATTGTTTCTTCACAATACCACACACC G A 562 ACAAATCATTACCTTTACACAAGGGTTGATAGCAGA 3871:23603 TTCTCCACTGTTTCTTTCTTGGCCTGCAGA AACATCAATGATGCTGTGTCATAAGGGCTAAACACA AGGATGCCATACATAATTAGCTCCAAAATA AAGTAACGGATGTCAATGGAACAACTAC AAAGTAAAAA scaffold 563 CGAGACGAGACGCGACCGTGGTTTTGAAAC C T 564 TTCTTTTCGCGGAAACCAAACAGGAAATACAATTGA 3:388526 CACAACAACAACAACTAGGGTTCATCCCTA CCATGTCGAAGAGGAAATTCGGATTCGAAGGCTTTG CCAAAAACCCCTCTTTACAATTCCTGCAGA GCATAAACCGCCAAACGACTTACAACTT TTTACCGCTT scaffold 565 GATTACCTTACAAACCGCATTCAAAATGGA A G 566 GTTAGTTTAGTCTGTTCAAATTTTCCGAATCTGAAG 4:729494 GGAACTGAGGTCGTCGAGGTAAATTTCTTT TAGTATGACTTTTGGTATCTCACTGAAATGTTCATT ATTTCTTTTTAGTTTGATGAATGCCTGCAG TTGGTATCTCAGTAAACCAAGTAATTGC TTCATTTGGA scaffold 567 CTGAGCTCCATTATCTATATAAACTCATGA C G 568 ATAAGATACCTTGTTTAAAACCAGAAAGATAAAATA 2283:29120 GCACTTCCGGACGACTTCTCAACGATATCC TAAGTTTTCGTTGTGATGAGTTTTTGGCATTTTCTA ACGGCTTCAAGGTAACAATAGTTTATCCTT ATCACTCTATTGGTTATGCTGCAGAGAG TCCACTGGTC scaffold 569 CTGGAACCACTAGCGAAGAAGCAGCGAAAG T C 570 ACACAACTCCTGGAGACAAAAATGTTCTGATCAGGT 4350:64549 TGACATCATTGCATTCTAATTGTTTGCCCC TAGAGATGCTCATGTGTCACATATTTATTTCGGGTA GGATATAGAATTGGGGCCCGATCACCCAAT GCTGGGTAGCCACTCCTTTTTTCACAGA TGTATGTAAC scaffold 571 TTTCTGAGGATGTTACAAGACATCCTGAGC T A 572 ATAGTTTATCCTTTCCACTGGTCGATAAGATACCTT 2283:29096 TCCATTATCTATATAAACTCATGAGCACTT GTTTAAAACCAGAAAGATAAAATATAAGTTTTCGTT CCGGACGACTTCTCAACGATATCCACGGCT GTGATGAGTTTTTGGCATTTTCTAATCA TCAAGGTAAC scaffold 573 AGGGGGATAATTGTACGACATTCGATGTTA A C 574 TGTGGTGTTGAATCCGGTGTCGTTTTGGCCCCTGCT 3469:17543 TGTCGTTTGGTGCAGTTGGAGATGGTGTGG GATTATTGTTTTAAAATTACTTCTACTATCTTTTCT CAGACGACACTGCAGCCTTTAAAGAGGCAT GGACCCTGCAGCCCCGGATTAATGTTCC GGAAAGCTGC scaffold 575 ACCCGTGATTCTCTGAAATCATTTTATTTT A T 576 GTATTTGTATGTTTGTGTAAGATAAATCATAAATTT 1022:170497 CCGTGCCTTATTACATAAGGAAGGAAGAAA CTAACGAACTCTTTAAACCACAGTTCCATGACCGCC AGAACTCGTATTTTGGGTTCTTTCCATCTT ACCACCTTCATCGACCGCCCGGTTATAT CGTATGTGTT scaffold 577 GAGTAGGAATGGGTTTCTTTGATCTCAATA C T 578 GGTTACTCCGGAGTTGCTTACAACCGTACCATCAAG 964:106240 TACCATATTTGGAGGCCTTGCCGTCTGATA GGTGTGATGTCAGAACGTGATCGTTGCTCCATTCCC AGGCTACTCGGATCAAGCTAGCTACTATGG CTTCTTACTCTCTCTTCTCTCCTCAAGC CCATGGAGCT scaffold 579 ATCATAAACTTATTTGGCTTAATCTGAAAA T A 580 ACCATGTAAACAGAGGTATCATTTGATGGAAGTGAA 1419:187788 TAGCCAACATAAATGATGAAATAACAGAAG GAGGCTGCAGGTAACACTTTGAATTTCCAATCAGGA AAAAGCAAGTAAATTTAAGAATTCAGCGAT ACGTATAGACCATATAATAACCCCGTGT GAAATTATCT scaffold 581 TTTCTAGCATTGGAGATGACATTGATATGG T A 582 GGGCTGCAGACTTTATAAGCAGCAATTCTTGCAGAG 3386:35408 TAATGATGTCGACACCATCAGCAATAGCGT GGAACTCCTCCTCTTGCAATGCCTTCTTTTAGTCCA CGTCAAAAGCTGCCAACATAGCTTCTGAAT TAGAAACTGACATTTTTTACATTGTTCC AGCACCCTGT scaffold 583 TATAATCTGCTCTTCTTGTTAGTATGTTTG G C 584 AGGATTGTGTTTGACATTTTCTTATCTTGGTGGAAA 575:241067 CCTTTTATATTCCGGGTAGATTTGTCTTAT CATTTTTAAGCAAACACGTGTTGCAGGCTTGACTAA TTAAAAACCCTTTCTGTGAGAAGACTTTTA TCTGATTTTCACGTGGAAGATTGAACTT TATGTATAGT scaffold 585 AGAATTTATACAGTAGAACCTCACTAATAT C G 586 TTGTTTATAAAATTTTAATCATTAAGAAACACAGCA 1863:93953 ATACGAAGAATAACCTCAAAAATTAAATCT AATAAACCTAACAAGTATTGAAAAATGTCCATTAAA TGGGCAGTTATAAATAAAAATAATTTTTAA AGAAACCATCGTTCTTTCCGGTCTTGAA ATTGTAAAAC scaffold 587 GACCATAAGACACTGCAGAGCTATGGCTCG G C 588 CCCCCCGGATCAGCACCGTGACCATGTTCTCCCGAG 575:459449 AATCACCACCATTTCCATTTTCTGTTGAGT TTCGAATGTGAACTATTATTCCCTCTGTATCGATTA TCAAATGCAAATTAGCATTCCCCCTGTACT GACTATACGAAGCTGAAACACTGTCATT GATAACTATG scaffold 589 TCTGTTTAAGGATTTCTGCAGCAATCGGGA T C 590 AGTGTCTTTACTATACCGGCATTGATGTTGAATAGG 773:155167 CGGTTGAGTTGACTGGATTACTGATTATGT TCATCACGAGTCATTCCAGGCTTTCTCGGAACTCCA GGATAAAGGCATCAGGGCAGTTGTCAGCAA GCAGGAATGACAACAACATTTACGCCTT CAGCCTCAAT scaffold 591 CCTTCTGTTTAAGGATTTCTGCAGCAATCG G A 592 ATCAGTGTCTTTACTATACCGGCATTGATGTTGAAT 773:155164 GGACGGTTGAGTTGACTGGATTACTGATTA AGGTCATCACGAGTCATTCCAGGCTTTCTCGGAACT TGTGGATAAAGGCATCAGGGCAGTTGTCAG CCAGCAGGAATGACAACAACATTTACGC CAACAGCCTC scaffold 593 TATTTGAATCCACTCAAGTCCACTTCACAA C T 594 CAACTCAAGTCCATGTAGTTGGTTGTTGATACTTGT 107:154377 TAAGTGGTTACAAGCTCACGCGGCCGGTGG GATTTACTTATATAAGAGTAACGATATGTGCACTCA TGTGAAGCTCACAATGCAACATTTGAGCCT AATTATGCATCAAAATATTAGATACAAT TTGTAGGGAT scaffold 595 GAACACACATCTTTCTCCGGCAACTTTAGT C T 596 ACCTTCAACTTCCTAATTGACAATGCATTTGGTAAT 371:34271 ACATTGCCGTTCAGTGCTTGCAGAAGCTTC GATTTTTTTTTTCTTCAGGTTACCTTGAAATTGTTC CTTCCAATAGCAGCAAGTACACATATTCGT ACATTTATAGCAGCATGAATGGTTGAAA GTGATGGATA scaffold 597 TAATAGTTCTTCTATTGCTGGTAATCGTCT A G 598 TTCTTCGCATCAGGTTCAGTTGCCCTTTATGTATTC 78:341641 GTGCTGAAGTGTCGGTGGTCCTCACCTACA TTGTACTCTATCAATTACTTGGTGTTTGACCTGCAG TGCATCTCTGCGTAGAGGATTGGCGGTGGT AGTTTGAGTGGACCCGTCTCCGCTGTAC GGTGGAAGGC scaffold 599 CCTATGTGATCGTCGCGAATGTGTTATCAA T A 600 GGGCGTAGTTGGATTGAAGTGCGCGGTAAGGTCCAC 156:85625 GTGCAGGAAGGTGGGAAGAAGTTTCTGAAG GAGTTCTTAGCCGGCGATCACATACACGAAATGAGG TGAGGAAGATGATGAAAAACCAGAGGGTGA GACGATATTTATAAGAAACTAACCGAGT AGAAGGAAGT

TABLE 10 Sample Sample Sample ID Name Type Reference for Reported Ancestry 1 Afghani indica http://medicannseeds.com/seed/afghani-regular/ Regular 2 Afghani indica http://medicannseeds.com/seed/afghani-regular/ Regular 3 Afghani indica http://medicannseeds.com/seed/afghani-regular/ Regular 4 Afghani indica http://medicannseeds.com/seed/afghani-regular/ Regular 5 Hindu indica https://www.kiwiseeds.com/kiwiseeds/kiwiseeds-hindu-kush-34671.html Kush 6 Pakistan indica https://www.cannabiogen.com/Producto/PAKISTAN%20CHITRAL%20KUSH%20-6.html Chitral Kush 7 Pakistan indica https://www.cannabiogen.com/Producto/PAKISTAN%20CHITRAL%20KUSH%20-6.html Chitral Kush 8 Ketama indica http://www.worldofseeds.eu/wos_en/ketama.html 9 Pure indica http://dnagenetics.com/seeds/pure-afghan Afghan 10 Enemy Of indica http://superstrains.biz/shop/enemy-of-the-state/ The State 11 Enemy Of indica http://superstrains.biz/shop/enemy-of-the-state/ The State 12 Enemy Of indica http://superstrains.biz/shop/enemy-of-the-state/ The State 13 Master indica http://homegrown-fantaseeds.com/product/masterkush Kush 14 Master indica http://homegrown-fantaseeds.com/product/masterkush Kush 15 Master indica http://whitelabelseeds.com/seeds/wlsc/master-kush Kush 16 Master indica http://whitelabelseeds.com/seeds/wlsc/master-kush Kush 17 Master indica http://whitelabelseeds.com/seeds/wlsc/master-kush Kush 18 Master indica http://whitelabelseeds.com/seeds/wlsc/master-kush Kush 19 Master indica http://whitelabelseeds.com/seeds/wlsc/master-kush Kush 20 Pakistan indica http://www.worldofseeds.eu/wos_es/pakistan-valley.html Valley 21 Pakistan indica http://www.worldofseeds.eu/wos_es/pakistan-valley.html Valley 22 Afghani indica http://homegrown-fantaseeds.com/product/afghani 23 Afghani indica http://homegrown-fantaseeds.com/product/afghani 24 Northern indica http://www.ministryofcannabis.com/feminized-cannabis-seeds/northern-lights-moc-feminized Lights 25 Northern indica http://www.ministryofcannabis.com/feminized-cannabis-seeds/northern-lights-moc-feminized Lights 26 Northern indica http://www.ministryofcannabis.com/feminized-cannabis-seeds/northern-lights-moc-feminized Lights 27 Hash indica http://www.seedsman.com/en/hash-passion-seeds Passion 28 Narkush indica http://www.seedsman.com/en/narkush-seeds 29 Narkush indica http://www.seedsman.com/en/narkush-seeds 30 Narkush indica http://www.seedsman.com/en/narkush-seeds 31 Narkush indica http://www.seedsman.com/en/narkush-seeds 32 Kush indica http://www.ceresseeds.com/online/en/regular-seeds/182-ceres-kush.html 33 Kush indica http://www.ceresseeds.com/online/en/regular-seeds/182-ceres-kush.html 34 Kush indica http://www.ceresseeds.com/online/en/regular-seeds/182-ceres-kush.html 35 Hindu indica https://sensiseeds.com/en/cannabis-seeds/sensi-seeds/hindu-kush Kush 36 Hindu indica https://sensiseeds.com/en/cannabis-seeds/sensi-seeds/hindu-kush Kush 37 Hindu indica https://sensiseeds.com/en/cannabis-seeds/sensi-seeds/hindu-kush Kush 38 Malawi sativa http://www.aceseeds.org/en/malawifem.html 39 Malawi sativa http://www.aceseeds.org/en/malawifem.html 40 Guatemala sativa http://www.aceseeds.org/en/guatemalastd.html 41 Guatemala sativa http://www.aceseeds.org/en/guatemalastd.html 42 Guatemala sativa http://www.aceseeds.org/en/guatemalastd.html 43 Malawi sativa http://www.seeds-of-africa.com/malawi-gold/ Gold 44 Malawi sativa http://www.seeds-of-africa.com/malawi-gold/ Gold 45 Malawi sativa http://www.seeds-of-africa.com/malawi-gold/ Gold 46 Malawi sativa http://www.seeds-of-africa.com/malawi-gold/ Gold 47 Pondo sativa http://www.seeds-of-africa.com/pondo-mystic/ Mystic 48 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold 49 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold 50 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold 51 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold 52 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold 53 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold 54 Durban sativa http://www.seeds-of-africa.com/durban-magic/ Magic 55 Mozambica sativa http://www.seeds-of-africa.com/mozambica/ 56 Mozambica sativa http://www.seeds-of-africa.com/mozambica/ 57 Mozambica sativa http://www.seeds-of-africa.com/mozambica/ 58 Mozambica sativa http://www.seeds-of-africa.com/mozambica/ 59 Transkei sativa http://www.seeds-of-africa.com/transkei/ 60 Transkei sativa http://www.seeds-of-africa.com/transkei/ 61 Transkei sativa http://www.seeds-of-africa.com/transkei/ 62 Transkei sativa http://www.seeds-of-africa.com/transkei/ 63 Zimbabwe sativa http://www.seeds-of-africa.com/zimbabwe/ 64 Zimbabwe sativa http://www.seeds-of-africa.com/zimbabwe/ 65 Zimbabwe sativa http://www.seeds-of-africa.com/zimbabwe/ 66 Lao sativa http://original-ssc.com/laos-luang-prabang-lao-sativa-seeds-ace-seeds.html Sativa 67 Lao sativa http://original-ssc.com/laos-luang-prabang-lao-sativa-seeds-ace-seeds.html Sativa 68 Purple sativa http://en.seedfinder.eu/strain-info/Purple_Haze/ACE_Seeds/ Haze 69 Purple sativa http://en.seedfinder.eu/strain-info/Purple_Haze/ACE_Seeds/ Haze 70 Zimbabwe sativa http://www.seeds-of-africa.com/zimbabwe/ 71 Malawi sativa http://www.seeds-of-africa.com/malawi-gold/ Gold 72 Malawi sativa http://www.seeds-of-africa.com/malawi-gold/ Gold 73 Durban sativa http://www.seeds-of-africa.com/durban-magic/ Magic 74 Durban sativa http://www.seeds-of-africa.com/durban-magic/ Magic 75 Durban sativa http://www.seeds-of-africa.com/durban-magic/ Magic 76 Durban sativa http://www.seeds-of-africa.com/durban-magic/ Magic 77 Durban sativa http://www.seeds-of-africa.com/durban-magic/ Magic 78 Pondo sativa http://www.seeds-of-africa.com/pondo-mystic/ Mystic 79 Pondo sativa http://www.seeds-of-africa.com/pondo-mystic/ Mystic 80 Pondo sativa http://www.seeds-of-africa.com/pondo-mystic/ Mystic 81 Pondo sativa http://www.seeds-of-africa.com/pondo-mystic/ Mystic 82 Pondo sativa http://www.seeds-of-africa.com/pondo-mystic/ Mystic 83 Coffee sativa http://www.seeds-of-africa.com/coffee-gold/ Gold 84 Coffee sativa http://www.seeds-of-africa.com/coffee-gold/ Gold 85 Coffee sativa http://www.seeds-of-africa.com/coffee-gold/ Gold 86 Coffee sativa http://www.seeds-of-africa.com/coffee-gold/ Gold 87 Mozambica sativa http://www.seeds-of-africa.com/mozambica/ 88 Mozambica sativa http://www.seeds-of-africa.com/mozambica/ 89 Mozambica sativa http://www.seeds-of-africa.com/mozambica/ 90 Mozambica sativa http://www.seeds-of-africa.com/mozambica/ 91 Mozambica sativa http://www.seeds-of-africa.com/mozambica/ 92 Mozambica sativa http://www.seeds-of-africa.com/mozambica/ 93 Transkei sativa http://www.seeds-of-africa.com/transkei/ 94 Transkei sativa http://www.seeds-of-africa.com/transkei/ 95 Transkei sativa http://www.seeds-of-africa.com/transkei/ 96 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold 97 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold 98 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold 99 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold 100 Swazi sativa http://www.seeds-of-africa.com/swazi-gold/ Gold

While the present application has been described with reference to what are presently considered to be the preferred examples, it is to be understood that the application is not limited to the disclosed examples. To the contrary, the application is intended to cover various modifications and equivalent arrangements included within the spirit and scope of the appended claims.

All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety. Specifically, the sequences associated with each accession numbers provided herein including for example accession numbers and/or biomarker sequences (e.g. protein and/or nucleic acid) provided in the Tables or elsewhere, are incorporated by reference in its entirely.

CITATIONS FOR REFERENCES REFERRED TO IN THE SPECIFICATION

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1. A method for detecting the presence or absence of each of a set of target alleles in a cannabis sample, the method comprising: I) obtaining a test sample comprising genomic DNA , and II) either i) genotyping the test sample for a set of single nucleotide polymorphisms (SNPs), the set comprising at least 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96, 100 or any number between and including 10-200 of the SNPs in Table 4 and/or 8, wherein each SNP comprises a major allele and a minor allele as provided in Table 4 and 8; and ii) detecting for each SNP of the set the presence or absence of the major allele and/or the minor allele in the test sample;major allele and/or or a) genotyping the test sample for a set of SNPs, the set at least 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96 or 100 of the comprising the SNPS in Table 5, wherein each SNP comprises a major allele and a minor allele as provided in Table 5; and b) detecting for each SNP of the set the presence or absence of the major allele and/or the minor allele in the test sample.
 2. The method of claim 1, wherein the set of SNPs comprises the SNPs in Table 4 and/or 8 with an Fst of greater than 0.712.
 3. The method of claim 1, wherein the set of SNPS comprises the SNPs in Table 5 with an Fst of greater than 0.679.
 4. The method of any one of claims 1 to 3, wherein the method further comprises displaying and/or providing a document displaying one or more features of the major and/or minor alleles.
 5. The method of claim 4, wherein the one or more features displayed is the minor allele nucleotide identity.
 6. The method of claim 4, wherein the method further comprises determining ancestry contribution of the test sample, optionally an ancestry contribution estimate or identification of ancestry dominance, wherein the ancestry dominance is selected from Cannabis sativa dominant or Cannabis indica dominant according to the set of target alleles detected in step II) ii).
 7. The method of claim 4, wherein the method further comprises identifying the test sample as marijuana or hemp, according to the set of target alleles detected in step b)
 8. The method of claim 1 for determining if a cannabis sample comprises Cannabis sativa and/or Cannabis indica, the method comprising: I) obtaining a test sample comprising genomic DNA , II) i) genotyping the test sample for a set of single nucleotide polymorphisms (SNPs), the set comprising at least 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96, 100 or any number between and including 10-200 of the SNPs in Table 4 and/or 8, wherein each SNP comprises a major allele and a minor allele as provided in Table 4 and 8; and ii) detecting for each SNP of the set the presence or absence of the major allele and/or the minor allele in the test sample;; and III) determining ancestry dominance of the test sample according to the set of target alleles detected in step II) ii and providing an estimate of the ancestry contribution or identifying the test sample as Cannabis sativa dominant Cannabis sativa or as Cannabis indica Cannabis indica dominant.
 9. The method of any one of claims 1 to 8, wherein the test sample is selected from a genomic DNA sample, a plant sample, a seed sample, leaf sample, a flower sample, a trichome sample, a pollen sample, and a sample of dried plant material including flower, pollen and trichomes.
 10. The method of any one of claims 1 to 8, wherein the obtaining the sample comprises isolating genomic DNA.
 11. The method of claim 9 or 10, wherein the test sample is marijuana.
 12. The method of claim 11, wherein the method further comprises selecting a breeding partner.
 13. The method of claim 1 for determining if a sample comprises hemp or marijuana, the method comprising I) obtaining a test sample comprising genomic DNA, II) a) genotyping the test sample for a set of single nucleotide polymorphisms (SNPs), the set comprising at least 10, 20, 30, 40, 48, 50, 60, 70, 80, 96 or 100 of the SNPs in Table 5, wherein each SNP comprises a major allele and a minor allele as provided in Table 5; and b) detecting detecting for each SNP of the set the presence or absence of the major allele and/or the minor allele in the test sample; major allele and/or and major allele and/or III) identifying whether the sample comprises hemp or marijuana according to the set of target alleles detected in step II) b).
 14. The method of claim 13, wherein the method is for differentiating drug and non-drug cannabis.
 15. The method of claim 1 for measuring genetic relatedness of a cannabis sample to Cannabis sativa reference and/or Cannabis indica reference, the method comprising: I) obtaining a test sample comprising genomic DNA , II) i) genotyping the test sample for a set of single nucleotide polymorphisms (SNPs), the set comprising at least 10, 20, 30, 40, 48, 50, 60, 70, 80, 90, 96, 100 or any number between and including 10-200 of the SNPs in Table 4 and/or 8, wherein each SNP comprises a major allele and a minor allele as provided in Table 4 and 8; and ii) detecting for each SNP of the set the presence or absence of the major allele and/or the minor allele in the test sample; III) calculating the genetic relatedness of the test sample to the Cannabis sativa reference and/or Cannabis indica reference according to the set of target alleles detected in step II) and IV) displaying and/or providing a document displaying the calculated genetic relatedness of the test sample.
 16. The method of claim 15, wherein the reference is a reference profile or database of reference profiles.
 17. The method of claims 15, wherein the reference is a reference sample.
 18. The method of claim 15 for measuring a genetic relatedness of a Cannabis sativa sample to a reference marijuana or reference hemp sample, the method comprising: I) obtaining a test sample comprising genomic DNA, II) a) genotyping the test sample for a set of single nucleotide polymorphisms (SNPs), the set comprising at least 10, 20, 30, 40, 48, 50, 60, 710, 80, 90, 96, or 100 of the SNPs in Table 5, wherein each SNP comprises a major allele and a minor allele as provided in Table 5; and b) detecting for each SNP of the set the presence or absence of the major allele and/or the minor allele in the test sample; III) calculating the genetic relatedness of the test sample to the marijuana reference and/or the hemp reference according to the set of target alleles detected in step II) b; and IV) displaying and/or providing a document displaying the calculated genetic relatedness of the test sample.
 19. The method of any one of claims 1 to 18, wherein the genotyping method comprises a PCR based method, optionally comprising DNA amplification using forward and reverse primers and/or primer extension.
 20. The method of any one of claims 6 to 18, wherein the method of determining ancestry contribution and/or identifying the sample comprises using a specifically programmed computer comprising an algorithm to compare the identity of the major and/or minor allele for each of the set of SNPs detected in the test sample to one or more cannabis reference profiles or a database comprising a plurality of cannabis reference profiles, each cannabis reference profile comprising genotype information of for the set of SNPs.
 21. The method of any one of claim 20, wherein the algorithm is comprises a principle components classifier or a fastStructure classifier.
 22. An isolated nucleic acid comprising at least 9, 12, 15 or at least 18 contiguous nucleotides of any one of SEQ ID Nos 1-200 and 401 to 600 or the complement thereof.
 23. A primer comprising the isolated nucleic acid of claim
 22. 24. The primer of claim 23, wherein the primer is a forward PCR primer that hybridizes with—or the complement or the reverse complement of residues 1-100 of any one of odd numbered SEQ ID Nos 1-600.
 25. The primer of claim 23, wherein the primer is a reverse PCR primer that hybridizes with or the complement or the reverse complement of residues 1 to 100 of any one of even numbered SEQ ID Nos 1-600.
 26. The primer of claim 23, wherein the primer is an allele specific primer for a major allele and/or a minor allele in Table 4, 5 or 8 and binds to residue 101 of any one of odd numbered SEQ ID Nos 1-600.
 27. The primer of claim 23 wherein the primer is a primer extension primer and binds to residue 101 of any one of any one of odd numbered SEQ ID Nos 1-600.
 28. The primer of any one of claims 23, to 27 further comprising a covalently bound tag, optionally a sequence specific nucleotide tail.
 29. A plurality of primers for detecting a SNP allele in Table 4, 5 and/or 8, wherein the plurality comprises as least 2 different primers selected from any one of claims 23 to
 27. 30. The plurality of primers of claim 29 wherein the plurality is a plurality of primer pairs.
 31. A kit comprising the isolated nucleic acid, primer or plurality of primers of any one of claims 23 to
 30. 32. The kit of claim 31 further comprising at least one reagent for an amplifying DNA.
 33. The kit of claim 31 or 32 further comprising at least one reagent for a primer extension reaction.
 34. An array comprising the isolated nucleic acid, primer or plurality of primers of any one of claims 23 to
 30. 